diff --git a/MetaMorpheus/EngineLayer/GlobalVariables.cs b/MetaMorpheus/EngineLayer/GlobalVariables.cs
index 2bf0a2017..3e8ccd4a0 100644
--- a/MetaMorpheus/EngineLayer/GlobalVariables.cs
+++ b/MetaMorpheus/EngineLayer/GlobalVariables.cs
@@ -70,7 +70,7 @@ public static class GlobalVariables
         public static void SetUpGlobalVariables()
         {
             AcceptedDatabaseFormats = new List<string> { ".fasta", ".fa", ".xml", ".msp" };
-            AcceptedSpectraFormats = new List<string> { ".raw", ".mzml", ".mgf", ".msalign" };
+            AcceptedSpectraFormats = new List<string> { ".raw", ".mzml", ".mgf", ".msalign", ".tdf", ".tdf_bin", ".d" };
             AnalyteType = AnalyteType.Peptide;
             _InvalidAminoAcids = new char[] { 'X', 'B', 'J', 'Z', ':', '|', ';', '[', ']', '{', '}', '(', ')', '+', '-' };
             ExperimentalDesignFileName = "ExperimentalDesign.tsv";
diff --git a/MetaMorpheus/GUI/App.xaml b/MetaMorpheus/GUI/App.xaml
index 7a7f81415..b01c43c56 100644
--- a/MetaMorpheus/GUI/App.xaml
+++ b/MetaMorpheus/GUI/App.xaml
@@ -9,7 +9,7 @@
         <SolidColorBrush x:Key="SideBarMainColor" Color="#353b48" />
         <SolidColorBrush x:Key="AccentColor" Color="#0097e6" />
         <SolidColorBrush x:Key="PurpleAccentColor" Color="#e6aeff" />
-        <SolidColorBrush x:Key="SecondaryButtonColor" Color="#2f3640" />
+        <SolidColorBrush x:Key="SecondaryButtonColor" Color="#504B59" />
         <SolidColorBrush x:Key="BackgroundColor" Color="#f5f6fa" />
         <SolidColorBrush x:Key="DataGridBackgroundColor" Color="#f5f6fa" />
         <SolidColorBrush x:Key="DataGridHeaderColor" Color="#dcdde1" />
diff --git a/MetaMorpheus/GUI/MainWindow.xaml.cs b/MetaMorpheus/GUI/MainWindow.xaml.cs
index 7f7f5769d..70eaa2fae 100644
--- a/MetaMorpheus/GUI/MainWindow.xaml.cs
+++ b/MetaMorpheus/GUI/MainWindow.xaml.cs
@@ -301,7 +301,7 @@ private void NewoutLabelStatus(object sender, StringEventArgs s)
             {
                 Dispatcher.BeginInvoke(new Action(() => NewoutLabelStatus(sender, s)));
             }
-            else
+            else if (InProgressTasks != null)
             {
                 // Find the task or the collection!!!
 
@@ -1279,7 +1279,7 @@ private void MenuItem_MetaDraw_Click(object sender, RoutedEventArgs e)
 
                 // Get search results
                 var searchResult = Directory.GetFiles(finalSearchTask.Task.OutputFolder)
-                    .First(p => p.EndsWith(".psmtsv") || p.EndsWith(".osmtsv"));
+                    .First(p => p.EndsWith("PSMs.psmtsv") || p.EndsWith("OSMs.osmtsv"));
 
                 filesToLoad = spectraFiles.Append(searchResult).ToArray();
             }
diff --git a/MetaMorpheus/GUI/MetaDraw/BioPolymerCoverageTabView.xaml b/MetaMorpheus/GUI/MetaDraw/BioPolymerCoverageTabView.xaml
new file mode 100644
index 000000000..c83f7bebf
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/BioPolymerCoverageTabView.xaml
@@ -0,0 +1,164 @@
+<UserControl x:Class="MetaMorpheusGUI.BioPolymerCoverageTabView"
+             xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+             xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+             xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" 
+             xmlns:d="http://schemas.microsoft.com/expression/blend/2008" 
+             xmlns:local="clr-namespace:MetaMorpheusGUI"
+             xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
+             xmlns:metaDraw="clr-namespace:GuiFunctions.MetaDraw;assembly=GuiFunctions"
+             mc:Ignorable="d" 
+             d:DataContext="{x:Static metaDraw:BioPolymerTabModel.Instance}"
+             d:DesignHeight="450" d:DesignWidth="800">
+    <DockPanel>
+        <Grid>
+            <Grid.ColumnDefinitions>
+                <ColumnDefinition Width="1*" />
+                <ColumnDefinition Width="Auto" />
+                <ColumnDefinition Width="3*" />
+            </Grid.ColumnDefinitions>
+
+            <!-- Left Side -->
+            <Grid Grid.Column="0">
+                <Grid.RowDefinitions>
+                    <RowDefinition Height="Auto"/>
+                    <RowDefinition Height="Auto"/>
+                    <RowDefinition Height="Auto"/>
+                    <RowDefinition Height="Auto"/>
+                    <RowDefinition Height="2*"/>
+                    <RowDefinition Height="25"/>
+                </Grid.RowDefinitions>
+
+                <!--Select database file-->
+                <DockPanel Grid.Row="0" LastChildFill="True" Grid.ColumnSpan="3" Margin="5 2">
+                    <Label Content="Database File: " Width="95" />
+
+                    <Button Content="Reset" HorizontalAlignment="Right" DockPanel.Dock="Right"
+                        VerticalAlignment="Center" Width="40" Height="26"
+                        IsEnabled="{Binding DatabasePath,  Converter={local:StringIsNotNullOrEmptyToBoolConverter}}"
+                        Command="{Binding ResetDatabaseCommand}" />
+
+                    <Button Name="SelectDatabaseButton"  Content="Select" HorizontalAlignment="Right" DockPanel.Dock="Right"
+                        VerticalAlignment="Center" Width="40" Height="26" Margin="5 0"
+                        IsEnabled="{Binding DatabasePath, Converter={local:StringIsNullOrEmptyToBoolConverter}}"
+                        Click="SelectDatabaseButton_OnClick" />
+
+                    <Label BorderThickness="1">
+                        <TextBlock TextTrimming="CharacterEllipsis">
+                            <TextBlock.Text>
+                                <Binding Path="DatabaseName" FallbackValue="None Selected" />
+                            </TextBlock.Text>
+                        </TextBlock>
+                    </Label>
+                </DockPanel>
+
+                <DockPanel Grid.Row ="1" Margin =" 5 2">
+                    <Label Content="Color By:" DockPanel.Dock="Left" />
+                    <ComboBox Width="120" Margin="5 0" DockPanel.Dock="Left" HorizontalAlignment="Left"
+                              SelectedValue="{Binding CoverageMapViewModel.ColorBy}" 
+                              ItemsSource="{Binding CoverageMapViewModel.AllColorByTypes}" />
+                </DockPanel>
+                
+
+
+                <!-- Load Button and Search Bar -->
+                <Border Grid.Row="2" Grid.ColumnSpan="3" BorderBrush="Black" 
+                    BorderThickness="0,0,0,1" Margin="5 2" >
+                    <DockPanel  LastChildFill="True" Margin="0 0 0 2">
+                        <Button Name="LoadDatabase" Content="Load Files" Width="80" 
+                                Command="{Binding LoadDatabaseCommand}"/>
+                        
+                        <TextBox Width="140"  DockPanel.Dock="Right" VerticalContentAlignment="Center"
+                                 Text="{Binding SearchText, UpdateSourceTrigger=PropertyChanged}" />
+                        <Label HorizontalAlignment="Right" Height="28">Search</Label>
+                    </DockPanel>
+                </Border>
+
+                <!-- Data Table -->
+                <GroupBox Header="BioPolymer Groups" Grid.Row="4" Margin="0 2">
+                    <Grid>
+                        <Grid.RowDefinitions>
+                            <RowDefinition Height="1*"/>
+                        </Grid.RowDefinitions>
+
+                        <DataGrid x:Name="biopolymerDataGrid" Grid.Row="0" AutoGenerateColumns="False" VerticalAlignment="Stretch" ScrollViewer.CanContentScroll="True" IsReadOnly="True" 
+                              CanUserDeleteRows="false" CanUserAddRows="false" SelectionMode="Single"
+                              SelectionChanged="BioPolymerDataGrid_OnSelectionChanged"
+                              ItemsSource="{Binding FilteredGroups}" 
+                              SelectedItem="{Binding SelectedGroup}">
+                            <DataGrid.Columns>
+                                <DataGridTextColumn Header="Accession" Binding="{Binding Accession}" Width="90" 
+                                                ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Unique Cov" Binding="{Binding UniqueSequenceCoverage, StringFormat={}{0:F2}}" Width="60" 
+                                                    ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Max Cov" Binding="{Binding MaximumSequenceCoverage, StringFormat={}{0:F2}}" Width="60" 
+                                                    ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Name" Binding="{Binding ProteinName}" Width="90" 
+                                                    ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Count" Binding="{Binding GroupCount}" Width="70" 
+                                                ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Length" Binding="{Binding Length}" Width="52" 
+                                                ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                            </DataGrid.Columns>
+                        </DataGrid>
+                    </Grid>
+                </GroupBox>
+
+                <!-- Loading overlay -->
+                <Grid x:Name="LoadOverlay" Grid.Row="4" Margin="2 16 2 4"
+                      Visibility="{Binding IsLoading, Converter={local:BooleanToVisibilityConverter}}"
+
+                      Background="#80000000"
+                      Panel.ZIndex="100">
+                    <StackPanel VerticalAlignment="Center" HorizontalAlignment="Center">
+                        <ProgressBar IsIndeterminate="True" Width="120" Height="18" Margin="0,0,0,8"/>
+                        <TextBlock Text="Loading..." Foreground="White" FontWeight="Bold" FontSize="16" HorizontalAlignment="Center"/>
+                    </StackPanel>
+                </Grid>
+
+                <!-- Export -->
+                <DockPanel Grid.Row="5" LastChildFill="True"  HorizontalAlignment="Center">
+                    <Label Content="Export As: "  DockPanel.Dock="Left"/>
+                    <Button Name="ExportBioPolymerCoverage" Width="40" HorizontalAlignment="Left"
+                            Style="{StaticResource MetaDrawButtonStyle}"
+                            Content="{Binding ExportType, Source={x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}}"
+                            Command="{Binding ExportImageCommand}"/>
+                </DockPanel>
+            </Grid>
+
+            <!--Moveable splitter-->
+            <GridSplitter Grid.Column="1" 
+                      HorizontalAlignment="Center"
+                      VerticalAlignment="Stretch"
+                      Background="Silver"
+                      Width="3"/>
+
+            <!-- Right side -->
+            <Grid Grid.Column="2" Name="BioPolymerAnnotationGrid" Style="{StaticResource InternalGridStyle}">
+                <Grid.RowDefinitions>
+                    <RowDefinition Height="Auto" />
+                    <RowDefinition Height="4*" />
+                    <RowDefinition Height="Auto" MaxHeight="300" />
+                </Grid.RowDefinitions>
+
+                <local:SettingsButtonControl Grid.Row="0" Height="52" x:Name="SettingsButton"
+                                                 HorizontalAlignment="Left" VerticalAlignment="Top"
+                                                 Panel.ZIndex="1" SelectedTabIndex="4" />
+                <!-- BioPolymer coverage display -->
+                <ScrollViewer Grid.Row="1" Name="BioPolymerCoverageHorizontalScroll" Width="Auto" 
+                              CanContentScroll="True" VerticalScrollBarVisibility="Auto" Margin="0 10 ">
+                    <local:BioPolymerCoverageMapView DataContext="{Binding CoverageMapViewModel}" />
+                </ScrollViewer>
+
+                <!-- Individual Results -->
+                <Expander Grid.Row="2" Header="Individual Results">
+                    <DataGrid ScrollViewer.CanContentScroll="True" IsReadOnly="True" 
+                              CanUserDeleteRows="false" CanUserAddRows="false" SelectionMode="Single"
+                              SelectionChanged="BioPolymerDataGrid_OnSelectionChanged"
+                              ItemsSource="{Binding SelectedGroup.CoverageResults}" >
+
+                    </DataGrid>
+                </Expander>
+            </Grid>
+        </Grid>
+    </DockPanel>
+</UserControl>
diff --git a/MetaMorpheus/GUI/MetaDraw/BioPolymerCoverageTabView.xaml.cs b/MetaMorpheus/GUI/MetaDraw/BioPolymerCoverageTabView.xaml.cs
new file mode 100644
index 000000000..f4a934905
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/BioPolymerCoverageTabView.xaml.cs
@@ -0,0 +1,55 @@
+using System.Linq;
+using EngineLayer;
+using System.Windows;
+using System.Windows.Controls;
+using GuiFunctions.MetaDraw;
+
+namespace MetaMorpheusGUI;
+
+/// <summary>
+/// Interaction logic for BioPolymerCoverageTabView.xaml
+/// </summary>
+public partial class BioPolymerCoverageTabView : UserControl
+{
+    public BioPolymerCoverageTabView()
+    {
+        InitializeComponent();
+    }
+
+    private void SelectDatabaseButton_OnClick(object sender, RoutedEventArgs e)
+    {
+        var dataContext = DataContext as BioPolymerTabViewModel;
+        if (sender == null || dataContext == null)
+        {
+            return;
+        }
+
+        string filterString = string.Join(";", GlobalVariables.AcceptedDatabaseFormats.Select(p => "*" + p));
+
+        Microsoft.Win32.OpenFileDialog openFileDialog1 = new Microsoft.Win32.OpenFileDialog
+        {
+            Filter = "Database Files(" + filterString + ")|" + filterString,
+            FilterIndex = 1,
+            RestoreDirectory = true,
+            Multiselect = false
+        };
+
+        if (openFileDialog1.ShowDialog() == true)
+        {
+            var toAdd = openFileDialog1.FileName;
+            if (GlobalVariables.AcceptedDatabaseFormats.Contains(GlobalVariables.GetFileExtension(toAdd).ToLowerInvariant()))
+            {
+                dataContext.DatabasePath = toAdd;
+            }
+            else
+            {
+                MessageBox.Show("Cannot read file type: " + GlobalVariables.GetFileExtension(toAdd).ToLowerInvariant());
+            }
+        }
+    }
+
+    private void BioPolymerDataGrid_OnSelectionChanged(object sender, SelectionChangedEventArgs e)
+    {
+        //throw new System.NotImplementedException();
+    }
+}
diff --git a/MetaMorpheus/GUI/MetaDraw/ChimeraAnalysisTabView.xaml.cs b/MetaMorpheus/GUI/MetaDraw/ChimeraAnalysisTabView.xaml.cs
index d5cd772ac..3c5ffdd14 100644
--- a/MetaMorpheus/GUI/MetaDraw/ChimeraAnalysisTabView.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/ChimeraAnalysisTabView.xaml.cs
@@ -105,11 +105,11 @@ private void AttachLegendCanvasEvents()
             if (legendCanvas != null)
             {
                 ChimeraLegend.Children.Add(dataContext?.LegendCanvas);
-
+                legendCanvas.UpdateLayout();
                 double parentWidth = ChimeraLegend.ActualWidth;
                 double parentHeight = ChimeraLegend.ActualHeight;
-                double legendWidth = legendCanvas.Width;
-                double legendHeight = legendCanvas.Height;
+                double legendWidth = legendCanvas.ActualWidth;
+                double legendHeight = legendCanvas.ActualHeight;
 
                 // Check if previous position is valid and within bounds
                 bool validLeft = !double.IsNaN(lastLeft) && lastLeft >= 0 && lastLeft + legendWidth <= parentWidth;
diff --git a/MetaMorpheus/GUI/MetaDraw/DeconExplorationTabView.xaml b/MetaMorpheus/GUI/MetaDraw/DeconExplorationTabView.xaml
new file mode 100644
index 000000000..945011e67
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/DeconExplorationTabView.xaml
@@ -0,0 +1,166 @@
+<UserControl x:Class="MetaMorpheusGUI.DeconExplorationTabView"
+             xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+             xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+             xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" 
+             xmlns:d="http://schemas.microsoft.com/expression/blend/2008" 
+             xmlns:local="clr-namespace:MetaMorpheusGUI"
+             xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions" 
+             xmlns:oxy="http://oxyplot.org/wpf"
+             mc:Ignorable="d" 
+             d:DataContext="{x:Static guiFunctions:DeconTabModel.Instance}"  
+             d:DesignHeight="450" d:DesignWidth="800">
+
+    <Grid>
+        <Grid.ColumnDefinitions>
+            <ColumnDefinition Width="*"/>
+            <ColumnDefinition Width="2"/>
+            <ColumnDefinition Width="3*"/>
+            <ColumnDefinition Width="2"/>
+            <ColumnDefinition Width="*"/>
+        </Grid.ColumnDefinitions>
+
+        <Grid.RowDefinitions>
+            <RowDefinition Height="*"/>
+            <RowDefinition Height="Auto"/>
+        </Grid.RowDefinitions>
+
+        <!-- Left: File and scan selection -->
+        <Grid Grid.Column="0" Grid.Row="0" Grid.RowSpan="2" Margin="8">
+            <Grid.RowDefinitions>
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="*" />
+                <RowDefinition Height="Auto" />
+            </Grid.RowDefinitions>
+            <Grid.ColumnDefinitions>
+                <ColumnDefinition Width="*" />
+                <ColumnDefinition Width="*" />
+            </Grid.ColumnDefinitions>
+            
+            <TextBlock Grid.Column="0" Grid.Row="0" Grid.ColumnSpan="2"  Text="Select Data File:" FontWeight="Bold" />
+            <ComboBox Grid.Column="0"  Grid.Row="1"  Grid.ColumnSpan="2" ItemsSource="{Binding MsDataFiles}"
+                      SelectedItem="{Binding SelectedMsDataFile}"
+                      DisplayMemberPath="FilePath" Margin="0,4,0,12" />
+
+
+            <TextBlock Grid.Column="0"  Grid.Row="2" Text="Deconvolution Mode:" FontWeight="Bold" />
+            <ComboBox Grid.Column="0"  Grid.Row="3" HorizontalContentAlignment="Center" VerticalContentAlignment="Center"
+                      SelectedValue="{Binding Mode}" 
+                      ItemsSource="{Binding DeconvolutionModes}" Margin="0,4,0,12" />
+            <StackPanel Grid.Column="1"  Grid.Row="3" Margin="10,4,10,12">
+                <CheckBox  Content="Display Annotations" FontWeight="DemiBold" HorizontalAlignment="Left"
+                           VerticalAlignment="Center" 
+                           IsChecked="{Binding DisplayIonAnnotations, Source={x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}}"/>
+                <CheckBox  Content="Identified Scans" FontWeight="DemiBold" HorizontalAlignment="Left"
+                           VerticalAlignment="Center" 
+                           IsChecked="{Binding OnlyIdentifiedScans}"/>
+            </StackPanel>
+
+            <StackPanel Grid.Column="0"  Grid.Row="4"  Grid.ColumnSpan="2" Orientation="Horizontal"
+                        Visibility="{Binding Mode, Converter={local:DeconModeToVisibilityConverter}}">
+                <StackPanel Orientation="Horizontal">
+                    <Label Content="Min m/z:"  FontWeight="Bold" VerticalAlignment="Center"/>
+                    <local:DoubleTextBoxControl Width="40" Margin="2" VerticalContentAlignment="Center"
+                                                Text="{Binding MinMzToPlot}" LowerBound="0"/>
+                </StackPanel>
+                <StackPanel Orientation="Horizontal">
+                    <Label Content="Max m/z:"  FontWeight="Bold" VerticalAlignment="Center"/>
+                    <local:DoubleTextBoxControl Width="40" Margin="2" VerticalContentAlignment="Center"
+                                                Text="{Binding MaxMzToPlot}" LowerBound="0"/>
+                </StackPanel>
+            </StackPanel>
+            
+            <TextBlock Grid.Column="0"  Grid.Row="5"  Grid.ColumnSpan="2" Text="Scans:" FontWeight="Bold" />
+            <DataGrid Grid.Column="0"  Grid.Row="6"  Grid.ColumnSpan="2" ItemsSource="{Binding Scans}"
+                      SelectedItem="{Binding SelectedMsDataScan}"
+                      SelectionMode="Single"
+                      SelectedCellsChanged="DataGrid_OnSelectedCellsChanged"
+                      AutoGenerateColumns="False"
+                      Margin="0,4,0,12"
+                      IsReadOnly="True"
+                      VerticalAlignment="Stretch">
+                <DataGrid.Columns>
+                    <DataGridTextColumn Header="Scan #" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                        Binding="{Binding OneBasedScanNumber}" Width="50" />
+                    <DataGridTextColumn Header="RT" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                        Binding="{Binding RetentionTime, StringFormat={}{0:F2}}" Width="40" />
+                    <DataGridTextColumn Header="MS Order" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                        Binding="{Binding MsnOrder}" Width="60" />
+                    <DataGridTextColumn Header="Isolation Mz" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                        Binding="{Binding IsolationMz, StringFormat={}{0:F2}}" Width="78" />
+                    <DataGridTextColumn Header="Precursor Scan #" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                        Binding="{Binding OneBasedPrecursorScanNumber}" Width="88" />
+                </DataGrid.Columns>
+            </DataGrid>
+
+            <!-- Loading overlay -->
+            <Grid x:Name="LoadingOverlay" Grid.Column="0"  Grid.Row="6"  Grid.ColumnSpan="2" Margin="0, 4, 0, 12"
+                  Visibility="{Binding IsLoading, Converter={local:BooleanToVisibilityConverter}}"
+                  Background="#80000000"
+                  Panel.ZIndex="100">
+                <StackPanel VerticalAlignment="Center" HorizontalAlignment="Center">
+                    <ProgressBar IsIndeterminate="True" Width="120" Height="18" Margin="0,0,0,8"/>
+                    <TextBlock Text="Loading..." Foreground="White" FontWeight="Bold" FontSize="16" HorizontalAlignment="Center"/>
+                </StackPanel>
+            </Grid>
+            
+            <Button Grid.Column="0"  Grid.Row="7"  Grid.ColumnSpan="2" Content="Run Deconvolution" Style="{StaticResource MetaDrawButtonStyle}"
+                    Command="{Binding RunDeconvolutionCommand}"
+                    CommandParameter="{Binding ElementName=DeconPlot}"
+                    Margin="0,8,0,0" />
+        </Grid>
+
+        <!-- Grid Splitter -->
+        <GridSplitter Grid.Column="1" Grid.Row="0" Width="2" HorizontalAlignment="Stretch" VerticalAlignment="Stretch"/>
+
+        <!-- Plot -->
+        <Grid Grid.Column="2" Grid.Row="0" >
+            <oxy:PlotView x:Name="DeconPlot" FontSize="16" FontStretch="Expanded" Margin="0 0 0 0"/>
+            <local:SettingsButtonControl Height="52" x:Name="SettingsButton"
+                                         HorizontalAlignment="Left" VerticalAlignment="Top"
+                                         Panel.ZIndex="1" SelectedTabIndex="0" />
+        </Grid>
+        <!-- Grid Splitter -->
+        <GridSplitter Grid.Column="3" Grid.Row="0" Width="2" HorizontalAlignment="Stretch" VerticalAlignment="Stretch"/>
+        
+        <!-- Right: Deconvoluted species -->
+        <DataGrid Grid.Column="4" Grid.Row="0" Grid.RowSpan="2"  ItemsSource="{Binding DeconvolutedSpecies}" AutoGenerateColumns="False" Margin="8" IsReadOnly="True">
+            <DataGrid.Columns>
+                <DataGridTemplateColumn Width="20">
+                    <DataGridTemplateColumn.CellTemplate>
+                        <DataTemplate>
+                            <Rectangle StrokeThickness="0"
+                                       Margin="0"
+                                       HorizontalAlignment="Stretch"
+                                       VerticalAlignment="Stretch"
+                                       Fill="{Binding Color, Converter={local:OxyColorToColorBrushConverter}}" />
+                        </DataTemplate>
+                    </DataGridTemplateColumn.CellTemplate>
+                </DataGridTemplateColumn>
+                <DataGridTextColumn Header="Mono Mass" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                    Binding="{Binding MonoisotopicMass, StringFormat={}{0:F2}}" Width="80"/>
+                <DataGridTextColumn Header="Mz (Most Abundant)" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                    Binding="{Binding MostAbundantMz, StringFormat={}{0:F2}}" Width="60"/>
+                <DataGridTextColumn Header="Z" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                    Binding="{Binding Charge}" Width="30"/>
+                <DataGridTextColumn Header="Intensity" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                    Binding="{Binding Intensity, StringFormat={}{0:F2}}" Width="70"/>
+                <DataGridTextColumn Header="Peaks" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                    Binding="{Binding PeakCount}" Width="40"/>
+                <DataGridTextColumn Header="Mz (Monoisotopic)" ElementStyle="{StaticResource DataGridCenteredCellStyle}"
+                                    Binding="{Binding MonoMz, StringFormat={}{0:F2}}" Width="60"/>
+                <DataGridTextColumn Header="Peak Mzs" 
+                                    Binding="{Binding PeakMzs}" Width="Auto"/>
+            </DataGrid.Columns>
+        </DataGrid>
+
+        <Expander Grid.Column="2" Grid.Row="1" Header="Deconvolution Parameters" IsExpanded="True">
+            <local:HostDeconParamControl Margin="8" 
+                                         DataContext="{Binding DeconHostViewModel}" />
+        </Expander>
+    </Grid>
+</UserControl>
diff --git a/MetaMorpheus/GUI/MetaDraw/DeconExplorationTabView.xaml.cs b/MetaMorpheus/GUI/MetaDraw/DeconExplorationTabView.xaml.cs
new file mode 100644
index 000000000..64b550271
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/DeconExplorationTabView.xaml.cs
@@ -0,0 +1,22 @@
+using GuiFunctions;
+using System.Windows.Controls;
+
+namespace MetaMorpheusGUI
+{
+    /// <summary>
+    /// Interaction logic for DeconExplorationTabView.xaml
+    /// </summary>
+    public partial class DeconExplorationTabView : UserControl
+    {
+        public DeconExplorationTabView()
+        {
+            InitializeComponent();
+        }
+
+        private void DataGrid_OnSelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
+        {
+            var dc = DataContext as DeconExplorationTabViewModel;
+            dc!.RunDeconvolutionCommand.Execute(DeconPlot);
+        }
+    }
+}
diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml
index 9ca3d9bee..1716c07eb 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml
@@ -7,6 +7,7 @@
         xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
         xmlns:local="clr-namespace:MetaMorpheusGUI"
         xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
+        xmlns:metaDraw="clr-namespace:GuiFunctions.MetaDraw;assembly=GuiFunctions"
         mc:Ignorable="d"
         Title="MetaDraw" 
         Closing="MetaDraw_OnClosing"
@@ -23,24 +24,97 @@
                     <Setter Property="Template">
                         <Setter.Value>
                             <ControlTemplate TargetType="TabItem">
-                                <Border Name="Border"
+                                <Border x:Name="Border"
                                         BorderThickness="1,1,1,0"
                                         BorderBrush="Gainsboro"
                                         CornerRadius="4,4,0,0"
                                         Margin="2,0"
                                         Height="{TemplateBinding Height}">
-                                    <ContentPresenter x:Name="ContentSite"
-                                                      VerticalAlignment="Center"
-                                                      HorizontalAlignment="Center"
-                                                      ContentSource="Header"
-                                                      Margin="10,2"/>
+                                    <Grid SnapsToDevicePixels="True" UseLayoutRounding="True">
+                                        <StackPanel Orientation="Horizontal"
+                                                    HorizontalAlignment="Center"
+                                                    VerticalAlignment="Center"
+                                                    Margin="10,2">
+                                            
+                                            <!-- Circular Spinner -->
+                                            <Grid x:Name="Spinner"
+                                                  Width="18" Height="18"
+                                                  Margin="0,0,6,0"
+                                                  Visibility="Collapsed">
+                                                <!-- Rotate entire spinner about its center so the green arc "tracks" the white ring -->
+                                                <Grid.RenderTransform>
+                                                    <RotateTransform x:Name="SpinnerRotate" Angle="0" CenterX="9"
+                                                                     CenterY="9" />
+                                                </Grid.RenderTransform>
+
+                                                <!-- White track: same circle as the arc (r=6), semi-transparent -->
+                                                <Ellipse Width="12" Height="12"
+                                                         HorizontalAlignment="Center"
+                                                         VerticalAlignment="Center"
+                                                         Stroke="White"
+                                                         StrokeThickness="3"
+                                                         Opacity="0.3"
+                                                         StrokeStartLineCap="Round"
+                                                         StrokeEndLineCap="Round" />
+
+                                                <!-- Green arc: verbose PathGeometry, exactly 120° sweep on the same r=6 circle -->
+                                                <Path x:Name="ProgressArc"
+                                                      Stroke="LimeGreen"
+                                                      StrokeThickness="3"
+                                                      StrokeStartLineCap="Round"
+                                                      StrokeEndLineCap="Round"
+                                                      StrokeLineJoin="Round"
+                                                      Fill="Transparent"
+                                                      Stretch="None">
+                                                    <Path.Data>
+                                                        <PathGeometry>
+                                                            <PathFigure StartPoint="9,3" IsClosed="False"
+                                                                        IsFilled="False">
+                                                                <ArcSegment Point="14.196,6"
+                                                                            Size="6,6"
+                                                                            RotationAngle="0"
+                                                                            IsLargeArc="False"
+                                                                            SweepDirection="Clockwise"
+                                                                            IsStroked="True" />
+                                                            </PathFigure>
+                                                        </PathGeometry>
+                                                    </Path.Data>
+                                                </Path>
+                                            </Grid>
+
+                                            <!-- Header Text -->
+                                            <ContentPresenter x:Name="ContentSite"
+                                                              VerticalAlignment="Center"
+                                                              HorizontalAlignment="Center"
+                                                              ContentSource="Header" />
+                                        </StackPanel>
+                                    </Grid>
                                 </Border>
+
+                                <ControlTemplate.Resources>
+                                    <Storyboard x:Key="SpinnerAnimation" RepeatBehavior="Forever">
+                                        <DoubleAnimation
+                                            Storyboard.TargetName="SpinnerRotate"
+                                            Storyboard.TargetProperty="Angle"
+                                            From="0" To="360" Duration="0:0:1" />
+                                    </Storyboard>
+                                </ControlTemplate.Resources>
+
                                 <ControlTemplate.Triggers>
                                     <Trigger Property="IsSelected" Value="True">
                                         <Setter TargetName="Border" Property="Background" Value="LightSkyBlue" />
                                     </Trigger>
                                     <Trigger Property="IsSelected" Value="False">
-                                        <Setter TargetName="Border" Property="Background" Value="{StaticResource BackgroundColor}" />
+                                        <Setter TargetName="Border" Property="Background"
+                                                Value="{StaticResource BackgroundColor}" />
+                                    </Trigger>
+                                    <Trigger Property="IsEnabled" Value="False">
+                                        <Setter TargetName="Border" Property="Background" Value="LightGray" />
+                                        <Setter TargetName="ContentSite" Property="Opacity" Value="0.5" />
+                                        <Setter TargetName="Spinner" Property="Visibility" Value="Visible" />
+                                        <Trigger.EnterActions>
+                                            <BeginStoryboard Storyboard="{StaticResource SpinnerAnimation}" />
+                                        </Trigger.EnterActions>
                                     </Trigger>
                                 </ControlTemplate.Triggers>
                             </ControlTemplate>
@@ -48,6 +122,8 @@
                     </Setter>
                 </Style>
             </TabControl.Resources>
+
+            <!-- Psm Tab -->
             <TabItem Header="PSM Annotation" Background="DarkGray">
                 <DockPanel>
                     <Grid>
@@ -153,17 +229,7 @@
                           VerticalAlignment="Stretch"
                           Background="Silver"
                           Width="3"/>
-
-                        <!--Loading progress popup-->
-                        <Popup IsOpen="False" x:Name="prgsFeed" Height="80" Width="300" PlacementTarget="{Binding ElementName=MetaDrawWindow}" Placement="Center">
-                            <Border Background="LightGray" CornerRadius="2" Height="78" Width="298" HorizontalAlignment="Center" VerticalAlignment="Center">
-                                <StackPanel Height="78" Background="LightGray">
-                                    <Label x:Name="prgsText" FontSize="20"></Label>
-                                    <ProgressBar IsIndeterminate="True" Height="20"></ProgressBar>
-                                </StackPanel>
-                            </Border>
-                        </Popup>
-
+                        
                         <!--PSM annotated peaks-->
                         <Grid Grid.Column="2">
                             <Grid.RowDefinitions>
@@ -288,7 +354,7 @@
                                         <Expander Grid.Row="1" VerticalAlignment="Bottom" IsExpanded="False" x:Name="AdditionalFragmentIonDisplay"
                                                    DataContext="{x:Type guiFunctions:FragmentationReanalysisViewModel}" Header="Fragment Reanalysis">
                                             <Expander.ToolTip>
-                                                Research the spectra file against the sequence with different fragment ions. 
+                                                Research the spectra file against the sequence with different fragment ions.
                                             </Expander.ToolTip>
                                             <local:FragmentReanalysisControl x:Name="AdditionalFragmentIonControl" DataContext="{Binding }" />
                                         </Expander>
@@ -447,13 +513,8 @@
                 </DockPanel>
             </TabItem>
 
-            <!-- Chimera Analysis tab -->
-            <TabItem Header="Chimera Annotation" Background="DarkGray" x:Name="ChimeraTab">
-                <local:ChimeraAnalysisTabView x:Name="ChimeraAnalysisTabView" />
-            </TabItem>
-            
             <!--Stats tab-->
-            <TabItem Header="Data Visualization" Background="DarkGray">
+            <TabItem Header="Data Visualization" x:Name="DataVisualizationTab"  Background="DarkGray">
                 <DockPanel>
                     <Grid>
                         <Grid.ColumnDefinitions>
@@ -484,7 +545,7 @@
                             </DockPanel>
 
                             <DockPanel Grid.Row="1" Margin="2">
-                                <Button Name="loadFilesStat" Content="Import Files From PSMTSV" Width="160" Click="loadFilesButtonStat_Click"/>
+                                <Button Name="loadFilesStat" Content="Import Files From PSMTSV" Width="160" Click="loadFilesButton_Click"/>
                             </DockPanel>
 
                             <!--Select psms to display by source file-->
@@ -558,6 +619,72 @@
                     </Grid>
                 </DockPanel>
             </TabItem>
+
+            <!-- BioPolymer Coverage tab-->
+            <TabItem Header="{Binding TabHeader}" IsEnabled="{Binding IsTabEnabled}" Background="DarkGray"
+                     d:DataContext="{d:DesignInstance metaDraw:BioPolymerTabModel, IsDesignTimeCreatable=True}"
+                     DataContext="{Binding BioPolymerTabViewModel, RelativeSource={RelativeSource AncestorType=Window}}">
+                <local:BioPolymerCoverageTabView x:Name="BioPolymerCoverageTabView" />
+            </TabItem>
+
+            <!-- Chimera Analysis tab -->
+            <TabItem Header="{Binding TabHeader}"  IsEnabled="{Binding IsTabEnabled}" Background="DarkGray" x:Name="ChimeraTab"
+                     d:DataContext="{d:DesignInstance metaDraw:ChimeraAnalysisTabViewModel, IsDesignTimeCreatable=True}"
+                     DataContext="{Binding ChimeraAnalysisTabViewModel, RelativeSource={RelativeSource AncestorType=Window}}">
+                <local:ChimeraAnalysisTabView x:Name="ChimeraAnalysisTabView" />
+            </TabItem>
+
+            <!--Deconvolution Exploration tab-->
+            <TabItem Header="{Binding TabHeader}"  IsEnabled="{Binding IsTabEnabled}" Background="DarkGray"
+                     d:DataContext="{d:DesignInstance guiFunctions:DeconExplorationTabViewModel, IsDesignTimeCreatable=True}"
+                     DataContext="{Binding DeconExplorationViewModel, RelativeSource={RelativeSource AncestorType=Window}}">
+                <local:DeconExplorationTabView x:Name="DeconExplorationTabView"/>
+            </TabItem>
         </TabControl>
+
+
+        <!--Loading progress popup-->
+        <Popup IsOpen="{Binding IsVisible}" Placement="Center" StaysOpen="True"
+       DataContext="{x:Static guiFunctions:LoadingProgressViewModel.Instance}" AllowsTransparency="True"
+       PopupAnimation="Fade">
+            <Border Background="LightGray" CornerRadius="6" Padding=" 8 12" 
+            MinWidth="420" MinHeight="160" BorderBrush="Gray" BorderThickness="2" SnapsToDevicePixels="True">
+                <StackPanel>
+                    <TextBlock Text="Loading Data..." FontSize="20" FontWeight="Bold" Margin="0,0,0,10"/>
+                    <ItemsControl ItemsSource="{Binding Steps}">
+                        <ItemsControl.ItemTemplate>
+                            <DataTemplate>
+                                <Grid Margin="0,4" HorizontalAlignment="Stretch">
+                                    <Grid.ColumnDefinitions>
+                                        <ColumnDefinition Width="*"/>
+                                        <ColumnDefinition Width="Auto"/>
+                                        <ColumnDefinition Width="Auto"/>
+                                        <ColumnDefinition Width="42"/>
+                                    </Grid.ColumnDefinitions>
+                                    <TextBlock Grid.Column="0" Text="{Binding StepName}" FontWeight="Bold" FontSize="14" VerticalAlignment="Center" Margin="0,0,5,0"/>
+                                    <TextBlock Grid.Column="1" Text="{Binding Current}" FontWeight="Normal" VerticalAlignment="Center" Margin="0,0,5,0"/>
+                                    <Grid Grid.Column="2" Width="120" Height="18" VerticalAlignment="Center">
+                                        <ProgressBar Minimum="0"
+                                             Maximum="{Binding Total}"
+                                             Value="{Binding Current}"
+                                             Height="18"
+                                             VerticalAlignment="Stretch"
+                                             Background="{StaticResource BackgroundColor}"
+                                             Foreground="LimeGreen"/>
+                                        <ProgressBar IsIndeterminate="True"
+                                             Height="18"
+                                             VerticalAlignment="Stretch"
+                                             Opacity="0.5"
+                                             Background="Transparent"
+                                             Foreground="Gray"/>
+                                    </Grid>
+                                    <TextBlock Grid.Column="3" Text="{Binding Total}" FontWeight="Normal" VerticalAlignment="Center" Margin="4,0,5,0"/>
+                                </Grid>
+                            </DataTemplate>
+                        </ItemsControl.ItemTemplate>
+                    </ItemsControl>
+                </StackPanel>
+            </Border>
+        </Popup>
     </Grid>
 </Window>
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
index 837c8b48d..cfebcf740 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
@@ -2,9 +2,11 @@
 using EngineLayer;
 using GuiFunctions;
 using GuiFunctions.MetaDraw;
+using Nett;
 using Omics.Fragmentation;
 using OxyPlot;
 using Readers;
+using Readers.InternalResults;
 using System;
 using System.Collections.Generic;
 using System.Collections.ObjectModel;
@@ -22,6 +24,7 @@
 using System.Windows.Data;
 using System.Windows.Input;
 using System.Windows.Media;
+using TaskLayer;
 
 namespace MetaMorpheusGUI
 {
@@ -37,11 +40,12 @@ public partial class MetaDraw : Window
         private ObservableCollection<string> PsmStatPlotFiles;
         public PtmLegendViewModel PtmLegend;
         private ObservableCollection<ModTypeForTreeViewModel> Modifications = new ObservableCollection<ModTypeForTreeViewModel>();
-        private static List<string> AcceptedSpectraFormats => SpectrumMatchFromTsvHeader.AcceptedSpectraFormats.Concat(new List<string> { ".msalign", ".tdf", ".tdf_bin" }).Select(format => format.ToLower()).ToList();
         private static List<string> AcceptedResultsFormats = new List<string> { ".psmtsv", ".tsv" };
         private static List<string> AcceptedSpectralLibraryFormats = new List<string> { ".msp" };
         private FragmentationReanalysisViewModel FragmentationReanalysisViewModel;
         public ChimeraAnalysisTabViewModel ChimeraAnalysisTabViewModel { get; set; }
+        public DeconExplorationTabViewModel DeconExplorationViewModel { get; set; }
+        public BioPolymerTabViewModel BioPolymerTabViewModel { get; set; }
 
         public MetaDraw(string[]? filesToLoad = null)
         {
@@ -49,16 +53,16 @@ public MetaDraw(string[]? filesToLoad = null)
 
             MetaDrawLogic = new MetaDrawLogic();
             SettingsButtonControl.SettingsChanged += RefreshPlotsAfterSettingsChange;
-            BindingOperations.EnableCollectionSynchronization(MetaDrawLogic.SpectralMatchResultFilePaths, MetaDrawLogic.ThreadLocker);
-            BindingOperations.EnableCollectionSynchronization(MetaDrawLogic.SpectraFilePaths, MetaDrawLogic.ThreadLocker);
-            BindingOperations.EnableCollectionSynchronization(MetaDrawLogic.FilteredListOfPsms, MetaDrawLogic.ThreadLocker);
-            BindingOperations.EnableCollectionSynchronization(MetaDrawLogic.SpectralMatchesGroupedByFile, MetaDrawLogic.ThreadLocker);
 
             itemsControlSampleViewModel = new ParentChildScanPlotsView();
             ParentChildScanViewPlots.DataContext = itemsControlSampleViewModel;
             AdditionalFragmentIonControl.DataContext = FragmentationReanalysisViewModel ??= new FragmentationReanalysisViewModel();
             AdditionalFragmentIonControl.LinkMetaDraw(this);
 
+            BioPolymerTabViewModel = new BioPolymerTabViewModel(MetaDrawLogic);
+            ChimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel();
+            DeconExplorationViewModel = new DeconExplorationTabViewModel(MetaDrawLogic);
+
             propertyView = new DataTable();
             propertyView.Columns.Add("Name", typeof(string));
             propertyView.Columns.Add("Value", typeof(string));
@@ -66,7 +70,6 @@ public MetaDraw(string[]? filesToLoad = null)
 
             dataGridScanNums.DataContext = MetaDrawLogic.PeptideSpectralMatchesView;
 
-
             Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
             base.Closing += this.OnClosing;
 
@@ -105,7 +108,7 @@ private void AddFile(string filePath)
         {
             var theExtension = GlobalVariables.GetFileExtension(filePath).ToLowerInvariant();
 
-            if (AcceptedSpectraFormats.Contains(theExtension))
+            if (GlobalVariables.AcceptedSpectraFormats.Contains(theExtension))
             {
                 // If a bruker timsTof file was selected, we actually want the parent folder
                 if(theExtension == ".tdf" || theExtension == ".tdf_bin")
@@ -164,6 +167,26 @@ private void AddFile(string filePath)
                     resetSpecLibraryButton.IsEnabled = true;
                 }
             }
+            else if (GlobalVariables.AcceptedDatabaseFormats.Contains(theExtension))
+            {
+                BioPolymerTabViewModel.DatabasePath = filePath;
+            }
+            else if (theExtension == ".txt" && filePath.Contains("AutoGeneratedManuscriptProse"))
+            {
+                var searchDirectory = Path.GetDirectoryName(filePath);
+                var proseFile = MetaMorpheusProseFile.LocateInDirectory(searchDirectory);
+                if (proseFile is not null)
+                {
+                    foreach (var spectraFile in proseFile.SpectraFilePaths)
+                    {
+                        AddFile(spectraFile);
+                    }
+                    foreach (var dbFile in proseFile.DatabasePaths)
+                    {
+                        AddFile(dbFile);
+                    }
+                }
+            }
             else
             {
                 MessageBox.Show("Cannot read file type: " + theExtension);
@@ -354,7 +377,7 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
 
         private void selectSpectraFileButton_Click(object sender, RoutedEventArgs e)
         {
-            string filterString = string.Join(";", AcceptedSpectraFormats.Select(p => "*" + p));
+            string filterString = string.Join(";", GlobalVariables.AcceptedSpectraFormats.Select(p => "*" + p));
 
             Microsoft.Win32.OpenFileDialog openFileDialog1 = new Microsoft.Win32.OpenFileDialog
             {
@@ -459,20 +482,17 @@ private void RefreshPlotsAfterSettingsChange(object sender, MetaDrawSettingsChan
 
             // save current selected PSM
             var selectedItem = dataGridScanNums.SelectedItem as SpectrumMatchFromTsv;
-            var selectedChimeraGroup = ChimeraAnalysisTabViewModel?.SelectedChimeraGroup;
+            var selectedChimeraGroup = ChimeraAnalysisTabViewModel.SelectedChimeraGroup;
 
             // filter based on new settings
             if (e.FilterChanged)
             {
                 MetaDrawLogic.FilterPsms();
+                ChimeraAnalysisTabViewModel.ProcessChimeraData(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles);
 
-                ChimeraAnalysisTabViewModel.ChimeraGroupViewModels.Clear();
-                foreach (var chimeraGroup in ChimeraAnalysisTabViewModel.ConstructChimericPsms(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles)
-                             .OrderByDescending(p => p.Count)
-                             .ThenByDescending(p => p.UniqueFragments)
-                             .ThenByDescending(p => p.TotalFragments))
+                foreach (var group in BioPolymerTabViewModel.AllGroups)
                 {
-                    ChimeraAnalysisTabViewModel.ChimeraGroupViewModels.Add(chimeraGroup);
+                    group.UpdatePropertiesAfterFilter();
                 }
             }
 
@@ -499,7 +519,11 @@ private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
         {
             // check for validity
             propertyView.Clear();
-            if (!MetaDrawLogic.SpectraFilePaths.Any())
+
+            bool loadSpectraFiles = true;
+            if ((e.Source as Button)?.Name == "loadFilesStat")
+                loadSpectraFiles = false;
+            else if (!MetaDrawLogic.SpectraFilePaths.Any())
             {
                 MessageBox.Show("Please add a spectra file.");
                 return;
@@ -513,22 +537,17 @@ private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
 
             // load the spectra file
             ToggleButtonsEnabled(false);
- 
-            prgsFeed.IsOpen = true;
-            prgsText.Content = "Loading data...";
-
-            // Add EventHandlers for popup click-in/click-out behaviour
-            Deactivated += new EventHandler(prgsFeed_Deactivator);
-            Activated += new EventHandler(prgsFeed_Reactivator);
-
-            var slowProcess = Task<List<string>>.Factory.StartNew(() => MetaDrawLogic.LoadFiles(loadSpectra: true, loadPsms: true));
-            await slowProcess;
 
-            string directoryPath = Path.Combine(Path.GetDirectoryName(MetaDrawLogic.SpectralMatchResultFilePaths.First()), "MetaDrawExport",
-                DateTime.Now.ToString("yyyy-MM-dd", CultureInfo.InvariantCulture));
-            ChimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles, directoryPath);
-            ChimeraTab.DataContext = ChimeraAnalysisTabViewModel;
-            var errors = slowProcess.Result;
+            dataGridScanNums.IsEnabled = false; // prevent clicking a psm before spectra and psms have loaded
+            var dataLoader = new MetaDrawDataLoader(MetaDrawLogic);
+            var errors = await dataLoader.LoadAllAsync(
+                loadSpectra: loadSpectraFiles,
+                loadPsms: true,
+                loadLibraries: true,
+                chimeraTabViewModel: ChimeraAnalysisTabViewModel,
+                bioPolymerTabViewModel: BioPolymerTabViewModel,
+                deconExplorationTabViewModel: DeconExplorationViewModel);
+            dataGridScanNums.IsEnabled = true;
 
             if (errors.Any())
             {
@@ -542,32 +561,9 @@ private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
                 PsmStatPlotFiles.Add(item.Key);
             }
 
-            // done loading - restore controls
-            this.prgsFeed.IsOpen = false;
-
-            // Remove added EventHandlers
-            Deactivated -= new EventHandler(prgsFeed_Deactivator);
-            Activated -= new EventHandler(prgsFeed_Reactivator);
-
             ToggleButtonsEnabled(true);
         }
 
-        /// <summary>
-        /// Deactivates the "loading data" popup if one clicks out of the main window
-        /// </summary>
-        private void prgsFeed_Deactivator(object sender, EventArgs e)
-        {
-            prgsFeed.IsOpen = false;
-        }
-
-        /// <summary>
-        /// Reactivates the "loading data" popup if one clicks into the main window
-        /// </summary>
-        private void prgsFeed_Reactivator(object sender, EventArgs e)
-        {
-            prgsFeed.IsOpen = true;
-        }
-
         private void TextBox_TextChanged(object sender, TextChangedEventArgs e)
         {
             string txt = (sender as TextBox).Text;
@@ -733,37 +729,6 @@ private void SetUpPlots()
             }
         }
 
-        private void loadFilesButtonStat_Click(object sender, RoutedEventArgs e)
-        {
-            // check for validity
-            if (!MetaDrawLogic.SpectralMatchResultFilePaths.Any())
-            {
-                MessageBox.Show("Please add a search result file.");
-                return;
-            }
-
-            (sender as Button).IsEnabled = false;
-            selectPsmFileButtonStat.IsEnabled = false;
-            resetPsmFileButtonStat.IsEnabled = false;
-            prgsFeedStat.IsOpen = true;
-
-            // load the PSMs
-            this.prgsTextStat.Content = "Loading data...";
-            MetaDrawLogic.LoadFiles(loadSpectra: false, loadPsms: true);
-
-            PsmStatPlotFiles.Clear();
-            foreach (var item in MetaDrawLogic.SpectralMatchesGroupedByFile)
-            {
-                PsmStatPlotFiles.Add(item.Key);
-            }
-
-            // done loading - restore controls
-            this.prgsFeedStat.IsOpen = false;
-            (sender as Button).IsEnabled = true;
-            selectPsmFileButtonStat.IsEnabled = true;
-            resetPsmFileButtonStat.IsEnabled = true;
-        }
-
         /// <summary>
         /// Export for Data Visualization tab
         /// </summary>
diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsChangedEventArgs.cs b/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsChangedEventArgs.cs
new file mode 100644
index 000000000..0962b2fe3
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsChangedEventArgs.cs
@@ -0,0 +1,9 @@
+using System;
+
+namespace MetaMorpheusGUI;
+
+public class MetaDrawSettingsChangedEventArgs : EventArgs
+{
+    public bool FilterChanged { get; set; } = false;
+    public bool DataVisualizationChanged { get; set; } = false;
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml b/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
index 9d1aaa5cf..618737657 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
@@ -614,6 +614,123 @@
                     </GroupBox>
                 </Grid>
             </TabItem>
+
+            <TabItem Header="BioPolymer Coverage">
+                <Grid>
+                    <Grid.ColumnDefinitions>
+                        <ColumnDefinition Width="2*" />
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="3*" />
+                    </Grid.ColumnDefinitions>
+
+                    <Grid.RowDefinitions>
+                        <RowDefinition Height="Auto" />
+                        <RowDefinition Height="Auto" />
+                        <RowDefinition Height="Auto" />
+                    </Grid.RowDefinitions>
+
+                    <StackPanel Grid.Column="0" Grid.Row="0" Margin="5 0 0 0">
+                        <GroupBox Header="Result Filtering">
+                            <StackPanel>
+                                <StackPanel Orientation="Vertical" Margin="5">
+                                    <CheckBox Content="Show decoys" Margin="5"
+                                              IsChecked="{Binding ShowDecoys}" />
+                                    <CheckBox Content="Show contaminants" Margin="5"
+                                              IsChecked="{Binding ShowContaminants}" />
+                                </StackPanel>
+
+                                <StackPanel Orientation="Horizontal" Margin="5">
+                                    <Label Content="Filter to q-value:" Width="120" />
+                                    <local:DoubleTextBoxControl Width="80" Height="24"
+                                                                VerticalContentAlignment="Center"
+                                                                HorizontalContentAlignment="Center"
+                                                                Text="{Binding QValueFilter}"
+                                                                LowerBound="0" UpperBound="1" />
+                                </StackPanel>
+
+                                <StackPanel Margin="5">
+                                    <Label Content="Filter to ambiguity level: " Width="140" />
+                                    <ComboBox Width="80"
+                                              ItemsSource="{Binding AmbiguityFilters}"
+                                              SelectedItem="{Binding AmbiguityFilter}" Height="24"
+                                              VerticalContentAlignment="Center" HorizontalContentAlignment="Center" />
+                                </StackPanel>
+
+                                <!-- glycan localization level -->
+                                <StackPanel>
+                                    <Label Content="Glycan Localization Level:" Margin="5" HorizontalAlignment="Center" />
+                                    <StackPanel Orientation="Horizontal" HorizontalAlignment="Center"
+                                                Margin="20 0 20 0">
+                                        <ComboBox Height="24"
+                                                  ItemsSource="{Binding GlycanLocalizationLevels}"
+                                                  SelectedItem="{Binding LocalizationLevelStart}" />
+                                        <ComboBox Height="24"
+                                                  ItemsSource="{Binding GlycanLocalizationLevels}"
+                                                  SelectedItem="{Binding LocalizationLevelEnd}" />
+                                    </StackPanel>
+                                </StackPanel>
+                            </StackPanel>
+                        </GroupBox>
+                        
+                        <!-- Export Options -->
+                        <GroupBox Header="ExportOptions">
+                            <StackPanel Orientation="Horizontal" HorizontalAlignment="Center">
+                                <Label Content="Export File Type:" Margin="0" HorizontalAlignment="Center" VerticalContentAlignment="Center"/>
+                                <ComboBox Height="24" HorizontalAlignment="Center" 
+                                          HorizontalContentAlignment="Center" Margin="0 0 10 0" 
+                                          ItemsSource="{Binding ExportTypes}" SelectedItem="{Binding ExportType}"/>
+                                <Label Content="Dpi:" Margin="0" HorizontalAlignment="Center" VerticalContentAlignment="Center"/>
+                                <local:DoubleTextBoxControl  Width="30" Height="24"
+                                                             Text="{Binding Dpi}" VerticalContentAlignment="Center"
+                                                             HorizontalContentAlignment="Center"/>
+                            </StackPanel>
+                        </GroupBox>
+                    </StackPanel>
+
+                    <GridSplitter Grid.Row="0" Grid.RowSpan="2" Grid.Column="1"
+                                  HorizontalAlignment="Center"
+                                  VerticalAlignment="Stretch"
+                                  Background="Silver"
+                                  Width="2" />
+
+                    <StackPanel Grid.Row="0" Grid.Column="2">
+                        <GroupBox Header="Colors">
+                            <ItemsControl ItemsSource="{Binding}" HorizontalContentAlignment="Stretch"
+                                          DataContext="{Binding BioPolymerCoverageColors}">
+                                <ItemsControl.ItemTemplate>
+                                    <DataTemplate>
+                                        <StackPanel Orientation="Horizontal">
+                                            <TextBlock Text="{Binding Name, FallbackValue='y - ion'}"
+                                                       Margin="0 0 15 0" Width="190" TextAlignment="Center" />
+                                            <Ellipse Width="12" Height="12"
+                                                     Stroke="{Binding ColorBrush, FallbackValue={StaticResource AccentColor}}"
+                                                     StrokeThickness="1"
+                                                     Fill="{Binding ColorBrush}" Margin="0 5 0 5" />
+                                            <ComboBox Width="100" HorizontalAlignment="Right" Margin="5 0 5 0"
+                                                      HorizontalContentAlignment="Center"
+                                                      SelectedItem="{Binding SelectedColor}"
+                                                      SelectionChanged="ComboBox_SelectionChanged_2"
+                                                      ItemsSource="{Binding Path=DataContext.PossibleColors, 
+                                                        RelativeSource={RelativeSource Mode=FindAncestor, 
+                                                        AncestorType={x:Type local:MetaDrawSettingsWindow}}}">
+                                            </ComboBox>
+                                        </StackPanel>
+                                    </DataTemplate>
+                                </ItemsControl.ItemTemplate>
+                            </ItemsControl>
+                        </GroupBox>
+                        <GroupBox  Header="Settings">
+                            <StackPanel Margin="5" Orientation="Horizontal">
+                                <Label Content="Text Size: " Width="80" />
+                                <local:IntegerTexBoxControl Width="80" Height="24"
+                                                            VerticalContentAlignment="Center"
+                                                            HorizontalContentAlignment="Center"
+                                                            Text="{Binding BioPolymerCoverageFontSize}"/>
+                            </StackPanel>
+                        </GroupBox>
+                    </StackPanel>
+                </Grid>
+            </TabItem>
         </TabControl>
         
 
diff --git a/MetaMorpheus/GUI/MetaDraw/SettingsButtonControl.xaml.cs b/MetaMorpheus/GUI/MetaDraw/SettingsButtonControl.xaml.cs
index f1216cb1b..f65801e51 100644
--- a/MetaMorpheus/GUI/MetaDraw/SettingsButtonControl.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/SettingsButtonControl.xaml.cs
@@ -91,10 +91,4 @@ private void SettingsButton_Click(object sender, RoutedEventArgs e)
 
         SettingsChanged?.Invoke(this, args);
     }
-}
-
-public class MetaDrawSettingsChangedEventArgs : EventArgs
-{
-    public bool FilterChanged { get; set; } = false;
-    public bool DataVisualizationChanged { get; set; } = false;
-}
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/MetaDraw/Views/BioPolymerCoverageMapView.xaml b/MetaMorpheus/GUI/MetaDraw/Views/BioPolymerCoverageMapView.xaml
new file mode 100644
index 000000000..b8260a0a8
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/Views/BioPolymerCoverageMapView.xaml
@@ -0,0 +1,16 @@
+<UserControl x:Class="MetaMorpheusGUI.BioPolymerCoverageMapView"
+             xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+             xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+             xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" 
+             xmlns:d="http://schemas.microsoft.com/expression/blend/2008" 
+             xmlns:local="clr-namespace:MetaMorpheusGUI"
+             mc:Ignorable="d" 
+             d:DesignHeight="450" d:DesignWidth="800">
+    <Grid>
+        <Image x:Name="CoverageImage"
+               Stretch="None"
+               HorizontalAlignment="Center"
+               VerticalAlignment="Top"
+               Source="{Binding CoverageDrawing}" />
+    </Grid>
+</UserControl>
diff --git a/MetaMorpheus/GUI/MetaDraw/Views/BioPolymerCoverageMapView.xaml.cs b/MetaMorpheus/GUI/MetaDraw/Views/BioPolymerCoverageMapView.xaml.cs
new file mode 100644
index 000000000..70f1de0ea
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/Views/BioPolymerCoverageMapView.xaml.cs
@@ -0,0 +1,31 @@
+using System.Windows;
+using System.Windows.Controls;
+using GuiFunctions;
+using GuiFunctions.MetaDraw;
+
+namespace MetaMorpheusGUI;
+
+/// <summary>
+/// Interaction logic for BioPolymerCoverageMapView.xaml
+/// </summary>
+public partial class BioPolymerCoverageMapView : UserControl
+{
+    private double _lastWidth = -1;
+    public BioPolymerCoverageMapView()
+    {
+        InitializeComponent();
+        this.SizeChanged += OnSizeChanged;
+    }
+
+    private BioPolymerCoverageMapViewModel ViewModel => DataContext as BioPolymerCoverageMapViewModel;
+
+    private void OnSizeChanged(object sender, SizeChangedEventArgs e)
+    {
+        // Only update if the UserControl's size actually changed
+        if (e.WidthChanged && this.ActualWidth > 0 && this.ActualWidth != _lastWidth)
+        {
+            _lastWidth = this.ActualWidth;
+            ViewModel?.UpdateLettersPerRow(this.ActualWidth);
+        }
+    }
+}
diff --git a/MetaMorpheus/GUI/Util/Converters/DeconModeToVisibilityConverter.cs b/MetaMorpheus/GUI/Util/Converters/DeconModeToVisibilityConverter.cs
new file mode 100644
index 000000000..89061a747
--- /dev/null
+++ b/MetaMorpheus/GUI/Util/Converters/DeconModeToVisibilityConverter.cs
@@ -0,0 +1,21 @@
+using System;
+using System.Globalization;
+using System.Windows;
+using GuiFunctions;
+
+namespace MetaMorpheusGUI;
+
+public class DeconModeToVisibilityConverter : BaseValueConverter<DeconModeToVisibilityConverter>
+{
+    public override object Convert(object value, Type targetType, object parameter, CultureInfo culture)
+    {
+        return value is DeconvolutionMode.FullSpectrum 
+            ? Visibility.Visible 
+            : Visibility.Collapsed;
+    }
+
+    public override object ConvertBack(object value, Type targetType, object parameter, CultureInfo culture)
+    {
+        throw new NotImplementedException();
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/Util/Converters/StringIsNotNullOrEmptyToBoolConverter.cs b/MetaMorpheus/GUI/Util/Converters/StringIsNotNullOrEmptyToBoolConverter.cs
new file mode 100644
index 000000000..dd2b459b9
--- /dev/null
+++ b/MetaMorpheus/GUI/Util/Converters/StringIsNotNullOrEmptyToBoolConverter.cs
@@ -0,0 +1,20 @@
+using System;
+using System.Globalization;
+
+namespace MetaMorpheusGUI;
+
+public class StringIsNotNullOrEmptyToBoolConverter : BaseValueConverter<StringIsNotNullOrEmptyToBoolConverter>
+{
+    public override object Convert(object value, Type targetType, object parameter, CultureInfo culture)
+    {
+        if (value is string str)
+        {
+            return !string.IsNullOrEmpty(str);
+        }
+        return true; // or false, depending on how you want to handle non-string inputs
+    }
+    public override object ConvertBack(object value, Type targetType, object parameter, CultureInfo culture)
+    {
+        throw new NotImplementedException();
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/Util/Converters/StringIsNullOrEmptyToBoolConverter.cs b/MetaMorpheus/GUI/Util/Converters/StringIsNullOrEmptyToBoolConverter.cs
new file mode 100644
index 000000000..e8bab8849
--- /dev/null
+++ b/MetaMorpheus/GUI/Util/Converters/StringIsNullOrEmptyToBoolConverter.cs
@@ -0,0 +1,20 @@
+using System;
+using System.Globalization;
+
+namespace MetaMorpheusGUI;
+
+public class StringIsNullOrEmptyToBoolConverter : BaseValueConverter<StringIsNullOrEmptyToBoolConverter>
+{
+    public override object Convert(object value, Type targetType, object parameter, CultureInfo culture)
+    {
+        if (value is string str)
+        {
+            return string.IsNullOrEmpty(str);
+        }
+        return true; // or false, depending on how you want to handle non-string inputs
+    }
+    public override object ConvertBack(object value, Type targetType, object parameter, CultureInfo culture)
+    {
+        throw new NotImplementedException();
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/Views/Deconvolution/ClassicDeconParamsControl.xaml b/MetaMorpheus/GUI/Views/Deconvolution/ClassicDeconParamsControl.xaml
index f0ac85d3e..b447f9efa 100644
--- a/MetaMorpheus/GUI/Views/Deconvolution/ClassicDeconParamsControl.xaml
+++ b/MetaMorpheus/GUI/Views/Deconvolution/ClassicDeconParamsControl.xaml
@@ -4,11 +4,9 @@
              xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" 
              xmlns:d="http://schemas.microsoft.com/expression/blend/2008" 
              xmlns:local="clr-namespace:MetaMorpheusGUI"
-             xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
              mc:Ignorable="d" 
              d:DesignHeight="60" d:DesignWidth="600">
-
-    <Grid d:DataContext="{x:Static guiFunctions:DeconParamsModel.Instance}" >
+    <Grid>
 
         <Grid.ColumnDefinitions>
             <ColumnDefinition Width="2*"/>
@@ -17,8 +15,13 @@
             <ColumnDefinition Width="*"/>
         </Grid.ColumnDefinitions>
 
-        <Label Content="Max Assumed Charge State:" Grid.Column="0" />
-        <local:IntegerTexBoxControl Grid.Column="1" x:Name="DeconvolutionMaxAssumedChargeStateTextBox"  Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"
+        <Grid.RowDefinitions>
+            <RowDefinition Height="*"/>
+            <RowDefinition Height="*"/>
+        </Grid.RowDefinitions>
+
+        <Label Content="Max Assumed Charge State:" Grid.Column="0" Grid.Row="0" />
+        <local:IntegerTexBoxControl Grid.Column="1" Grid.Row="0" x:Name="DeconvolutionMaxAssumedChargeStateTextBox"  Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"
                                     Text="{Binding MaxAssumedChargeState}" HorizontalContentAlignment="Center" VerticalContentAlignment="Center" AllowNegative="True">
             <TextBox.ToolTip>
                 <TextBlock>
@@ -27,8 +30,8 @@
             </TextBox.ToolTip>
         </local:IntegerTexBoxControl>
 
-        <Label Content="Min Assumed Charge State:" Grid.Column="2" />
-        <local:IntegerTexBoxControl Grid.Column="3"   Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" HorizontalAlignment="Left"
+        <Label Content="Min Assumed Charge State:" Grid.Column="2" Grid.Row="0"/>
+        <local:IntegerTexBoxControl Grid.Column="3" Grid.Row="0" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" HorizontalAlignment="Left"
                                     Text="{Binding MinAssumedChargeState}" HorizontalContentAlignment="Center" VerticalContentAlignment="Center" AllowNegative="True">
             <TextBox.ToolTip>
                 <TextBlock>
@@ -36,5 +39,25 @@
                 </TextBlock>
             </TextBox.ToolTip>
         </local:IntegerTexBoxControl>
+
+        <Label Content="Deconvolution Tolerance (ppm):" Grid.Column="0" Grid.Row="1" />
+        <local:DoubleTextBoxControl Grid.Column="1" Grid.Row="1" x:Name="DeconvolutionTolerancePpmStateTextBox"  Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" 
+                                    Text="{Binding DeconvolutionTolerancePpm}" HorizontalContentAlignment="Center" VerticalContentAlignment="Center" >
+            <TextBox.ToolTip>
+                <TextBlock>
+                    Tolerance in m/z space used to group isotopic peaks into an envelope.
+                </TextBlock>
+            </TextBox.ToolTip>
+        </local:DoubleTextBoxControl>
+
+        <Label Content="Intensity Ratio Limit:" Grid.Column="2" Grid.Row="1"/>
+        <local:DoubleTextBoxControl Grid.Column="3" Grid.Row="1" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" HorizontalAlignment="Left"
+                                    Text="{Binding IntensityRatioLimit}" HorizontalContentAlignment="Center" VerticalContentAlignment="Center">
+            <TextBox.ToolTip>
+                <TextBlock>
+                    The maximum allowed ratio between each subsequent peak in an isotopic envelope. For example, if the ratio is 10, each peak in the envelope must be at least 1/10th the intensity of the previous peak.
+                </TextBlock>
+            </TextBox.ToolTip>
+        </local:DoubleTextBoxControl>
     </Grid>
 </UserControl>
diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj.DotSettings b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj.DotSettings
index 941e74a11..5afbf7160 100644
--- a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj.DotSettings
+++ b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj.DotSettings
@@ -1,3 +1,4 @@
 <wpf:ResourceDictionary xml:space="preserve" xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" xmlns:s="clr-namespace:System;assembly=mscorlib" xmlns:ss="urn:shemas-jetbrains-com:settings-storage-xaml" xmlns:wpf="http://schemas.microsoft.com/winfx/2006/xaml/presentation">
-	<s:Boolean x:Key="/Default/CodeInspection/NamespaceProvider/NamespaceFoldersToSkip/=chimeras/@EntryIndexedValue">True</s:Boolean></wpf:ResourceDictionary>
-	<s:Boolean x:Key="/Default/CodeInspection/NamespaceProvider/NamespaceFoldersToSkip/=viewmodels/@EntryIndexedValue">True</s:Boolean></wpf:ResourceDictionary>
\ No newline at end of file
+	<s:Boolean x:Key="/Default/CodeInspection/NamespaceProvider/NamespaceFoldersToSkip/=chimeras/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/CodeInspection/NamespaceProvider/NamespaceFoldersToSkip/=metadraw_005Cbiopolymercoverage/@EntryIndexedValue">True</s:Boolean></wpf:ResourceDictionary>
+	
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageMapViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageMapViewModel.cs
new file mode 100644
index 000000000..530d0e15a
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageMapViewModel.cs
@@ -0,0 +1,605 @@
+using GuiFunctions.Util;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Windows;
+using System.Windows.Media;
+
+namespace GuiFunctions.MetaDraw;
+
+public enum ColorResultsBy
+{
+    None,
+    CoverageType,
+    FileOrigin,
+}
+
+public class BioPolymerCoverageMapViewModel : BaseViewModel
+{
+
+    #region Color Handling
+
+    private static readonly CyclicalQueue<SolidColorBrush> ColorQueue = new(new[]
+    {
+        new SolidColorBrush(Colors.Red),
+        new SolidColorBrush(Colors.Blue),
+        new SolidColorBrush(Colors.Green),
+        new SolidColorBrush(Colors.Orange),
+        new SolidColorBrush(Colors.Purple),
+        new SolidColorBrush(Colors.Teal),
+        new SolidColorBrush(Colors.Brown),
+        new SolidColorBrush(Colors.Pink),
+        new SolidColorBrush(Colors.Yellow),
+        new SolidColorBrush(Colors.Gray),
+        new SolidColorBrush(Colors.Cyan),
+        new SolidColorBrush(Colors.Magenta),
+        new SolidColorBrush(Colors.LimeGreen),
+        new SolidColorBrush(Colors.DarkBlue),
+        new SolidColorBrush(Colors.DarkRed),
+        new SolidColorBrush(Colors.DarkGreen),
+        new SolidColorBrush(Colors.Gold),
+        new SolidColorBrush(Colors.Indigo),
+        new SolidColorBrush(Colors.Olive),
+        new SolidColorBrush(Colors.Maroon),
+        new SolidColorBrush(Colors.Navy),
+        new SolidColorBrush(Colors.Turquoise),
+        new SolidColorBrush(Colors.Violet),
+        new SolidColorBrush(Colors.Sienna),
+        new SolidColorBrush(Colors.Salmon),
+        new SolidColorBrush(Colors.Coral),
+        new SolidColorBrush(Colors.Khaki),
+        new SolidColorBrush(Colors.Plum),
+        new SolidColorBrush(Colors.Peru),
+        new SolidColorBrush(Colors.SteelBlue),
+        new SolidColorBrush(Colors.MediumPurple),
+        new SolidColorBrush(Colors.MediumSeaGreen),
+        new SolidColorBrush(Colors.MediumSlateBlue),
+        new SolidColorBrush(Colors.MediumVioletRed),
+        new SolidColorBrush(Colors.MediumOrchid),
+        new SolidColorBrush(Colors.MediumTurquoise),
+        new SolidColorBrush(Colors.MediumSpringGreen),
+        new SolidColorBrush(Colors.MediumAquamarine)
+    });
+
+    private static readonly Dictionary<string, SolidColorBrush> IdentifierToColor = [];
+
+    public ColorResultsBy[] AllColorByTypes { get; } = Enum.GetValues<ColorResultsBy>();
+
+    private ColorResultsBy _colorBy = ColorResultsBy.CoverageType;
+    public ColorResultsBy ColorBy
+    {
+        get => _colorBy;
+        set
+        {
+            if (_colorBy != value)
+            {
+                _colorBy = value;
+                OnPropertyChanged(nameof(ColorBy));
+                IdentifierToColor.Clear();
+                ColorQueue.Reset();
+                Redraw();
+            }
+        }
+    }
+
+    private SolidColorBrush GetColorBrush(BioPolymerCoverageResultModel result)
+    {
+        switch (_colorBy)
+        {
+            case ColorResultsBy.CoverageType:
+                return MetaDrawSettings.BioPolymerCoverageColors[result.CoverageType];
+            case ColorResultsBy.FileOrigin:
+                // Use FileName as identifier since FullFilePath is not available
+                return GetColorByIdentifier(result.Match.FileName);
+            default:
+                return new SolidColorBrush(Colors.Gray);
+        }
+    }
+
+    // Helper method for FileOrigin coloring
+    private SolidColorBrush GetColorByIdentifier(string identifier)
+    {
+        if (string.IsNullOrEmpty(identifier))
+            return new SolidColorBrush(Colors.Gray);
+
+        if (!IdentifierToColor.TryGetValue(identifier, out var brush))
+        {
+            brush = ColorQueue.Dequeue();
+            IdentifierToColor[identifier] = brush;
+        }
+        return brush;
+    }
+
+    #endregion
+
+    private DrawingImage _coverageDrawing;
+    public DrawingImage CoverageDrawing
+    {
+        get => _coverageDrawing;
+        internal set { _coverageDrawing = value; OnPropertyChanged(nameof(CoverageDrawing)); }
+    }
+
+    private BioPolymerGroupViewModel _group;
+    public BioPolymerGroupViewModel Group
+    {
+        get => _group;
+        set { _group = value; OnPropertyChanged(nameof(Group)); Redraw(); }
+    }
+
+    private int _lettersPerRow = 50;
+    public int LettersPerRow
+    {
+        get => _lettersPerRow;
+        set { _lettersPerRow = value; OnPropertyChanged(nameof(LettersPerRow)); }
+    }
+
+    private double _availableWidth = 800; // Default, should be set by view on resize
+    public double AvailableWidth
+    {
+        get => _availableWidth;
+        set { _availableWidth = value; OnPropertyChanged(nameof(AvailableWidth)); UpdateLettersPerRow(value); }
+    }
+
+    // Call this from the view when the canvas size changes
+    public void UpdateLettersPerRow(double availableWidth)
+    {
+        _availableWidth = availableWidth;
+        int newLetters = Math.Max(10, (int)(availableWidth / (MetaDrawSettings.BioPolymerCoverageFontSize * 0.70)));
+        if (newLetters != LettersPerRow)
+            LettersPerRow = newLetters;
+        else
+            Redraw();
+    }
+
+    private void Redraw()
+    {
+        if (Group == null)
+        {
+            CoverageDrawing = null;
+            return;
+        }
+
+        var seq = Group.Sequence;
+        var results = Group.CoverageResults;
+        var filteredResults = results.Where(p => MetaDrawSettings.FilterAcceptsPsm(p.Match)).ToList();
+        int lettersPerRow = LettersPerRow;
+        var bioPolymerName = Group.ProteinName;
+        double fontSize = MetaDrawSettings.BioPolymerCoverageFontSize;
+
+        double plotMargin = fontSize * 2;
+        double usableWidth = Math.Max(1, AvailableWidth - 2 * plotMargin);
+        double letterWidth = usableWidth / lettersPerRow;
+        double letterHeight = fontSize * 1.2;
+        double rectHeight = fontSize * 0.8;
+        double yPad = fontSize * 0.2;
+        double rectJitter = rectHeight * 0.5;
+
+        int nRows = (seq.Length + lettersPerRow - 1) / lettersPerRow;
+        var rowRectangles = new Dictionary<int, List<(int startCol, int endCol)>>();
+        var rowOccupancy = new Dictionary<int, int[]>(); // row -> per-column track usage
+
+        var dv = new DrawingVisual();
+        using (var dc = dv.RenderOpen())
+        {
+            double legendSpacing = fontSize * 0.5;
+            double dpi = MetaDrawSettings.CanvasPdfExportDpi;
+            double headerTop = legendSpacing;
+
+            // --- Draw BioPolymer Name at the very top ---
+            var bioPolymerNameText = new FormattedText(
+                bioPolymerName,
+                System.Globalization.CultureInfo.CurrentCulture,
+                FlowDirection.LeftToRight,
+                new Typeface("Segoe UI Bold"),
+                fontSize * 1.1,
+                Brushes.Black,
+                dpi);
+
+            double nameX = plotMargin + (usableWidth - bioPolymerNameText.Width) / 2;
+            double nameY = legendSpacing; // Start at the top margin
+            dc.DrawText(bioPolymerNameText, new Point(nameX, nameY));
+
+            // --- Global coverage metrics ---
+            int seqLen = seq.Length;
+            var anyCovered = new bool[seqLen];
+            var uniqueCovered = new bool[seqLen];
+
+            foreach (var r in filteredResults)
+            {
+                bool isUnique = r.CoverageType == BioPolymerCoverageType.Unique
+                             || r.CoverageType == BioPolymerCoverageType.UniqueMissedCleavage;
+
+                int s = Math.Max(1, r.Start) - 1;
+                int e = Math.Min(seqLen, r.End) - 1;
+                for (int i = s; i <= e; i++)
+                {
+                    anyCovered[i] = true;
+                    if (isUnique) uniqueCovered[i] = true;
+                }
+            }
+            int uniqueCoveredCount = uniqueCovered.Count(b => b);
+            int maxCoveredCount = anyCovered.Count(b => b);
+
+            var metricsText = $"Unique Coverage: {uniqueCoveredCount}/{seqLen} ({Math.Round(100 * uniqueCoveredCount / (double)seqLen, 2)}%)   |   Maximum Coverage: {maxCoveredCount}/{seqLen} ({Math.Round(100 * maxCoveredCount / (double)seqLen, 2)}%)";
+            var metricsFt = new FormattedText(
+                metricsText,
+                System.Globalization.CultureInfo.CurrentCulture,
+                FlowDirection.LeftToRight,
+                new Typeface("Segoe UI"),
+                fontSize * 0.9,
+                Brushes.Black,
+                dpi);
+
+            double metricsX = plotMargin + (usableWidth - metricsFt.Width) / 2;
+            double metricsY = nameY + bioPolymerNameText.Height + legendSpacing * 0.5;
+            dc.DrawText(metricsFt, new Point(metricsX, metricsY));
+
+            // --- Legend, wrapped ---
+            var sep = new FormattedText("\t", System.Globalization.CultureInfo.CurrentCulture, FlowDirection.LeftToRight, new Typeface("Segoe UI"), fontSize * 0.8, Brushes.DimGray, dpi);
+            var sepWidth = sep.Width;
+
+            double legendY = metricsY + metricsFt.Height + legendSpacing;
+            var legendItems = CreateLegendItems(filteredResults, fontSize, dpi, ColorBy);
+
+            var legendLines = WrapLegendItems(legendItems, fontSize, usableWidth, sepWidth);
+
+            double legendLineHeight = legendItems.Count == 0 ? 0 : Math.Max(fontSize * 0.8, legendItems.Max(li => li.Text.Height));
+            
+
+            foreach (var line in legendLines)
+            {
+                double lineWidth = line.Sum(item => fontSize * 0.8 + 6 + item.Text.Width) + sepWidth * (line.Count - 1);
+                double legendX = plotMargin + (usableWidth - lineWidth) / 2;
+                for (int i = 0; i < line.Count; i++)
+                {
+                    var (brush, text) = line[i];
+                    var rect = new Rect(legendX, legendY + (legendLineHeight - fontSize * 0.8) / 2, fontSize * 0.8, fontSize * 0.8);
+                    dc.DrawRoundedRectangle(brush, null, rect, 4, 4);
+                    legendX += fontSize * 0.8 + 6;
+
+                    double textY = legendY + (legendLineHeight - text.Height) / 2;
+                    dc.DrawText(text, new Point(legendX, textY));
+                    legendX += text.Width;
+
+                    if (i < line.Count - 1)
+                    {
+                        double sepY = legendY + (legendLineHeight - text.Height) / 2;
+                        dc.DrawText(sep, new Point(legendX, sepY));
+                        legendX += sepWidth;
+                    }
+                }
+                legendY += legendLineHeight + legendSpacing * 0.2;
+            }
+
+            // --- Offset plot below header block (metrics + legend) ---
+            double headerBlockHeight = bioPolymerNameText.Height + metricsFt.Height + legendSpacing + legendLines.Count * (legendLineHeight + legendSpacing * 0.2);
+            double plotYOffset = headerTop + headerBlockHeight + legendSpacing;
+            var drawnRects = new HashSet<(int row, int startCol, int endCol)>();
+
+            // --- Draw rectangles for each peptide, with jitter for overlaps ---
+            foreach (var res in filteredResults)
+            {
+                int startIdx = res.Start - 1;
+                int endIdx = res.End - 1;
+                int len = endIdx - startIdx + 1;
+
+                int idx = startIdx;
+                int remaining = len;
+                int row = idx / lettersPerRow;
+                int col = idx % lettersPerRow;
+
+                bool isFirstSegment = true;
+                while (remaining > 0)
+                {
+                    int drawLen = Math.Min(remaining, lettersPerRow - col);
+                    int thisStartCol = col;
+                    int thisEndCol = col + drawLen - 1;
+
+                    // Cache drawn rectangles to avoid duplicates
+                    var rectKey = (row, thisStartCol, thisEndCol);
+                    if (!drawnRects.Add(rectKey))
+                    {
+                        // Skip duplicate rectangle
+                        remaining -= drawLen;
+                        idx += drawLen;
+                        row++;
+                        col = 0;
+                        isFirstSegment = false;
+                        continue;
+                    }
+
+                    // Keep rects if you need them elsewhere (optional)
+                    if (!rowRectangles.TryGetValue(row, out var rects))
+                    {
+                        rects = new List<(int, int)>();
+                        rowRectangles[row] = rects;
+                    }
+                    rects.Add((thisStartCol, thisEndCol));
+
+                    // Per-row, per-column occupancy: first plotted at a column gets track 0.
+                    // Only overlapping residues force indent > 0.
+                    if (!rowOccupancy.TryGetValue(row, out var occ))
+                    {
+                        occ = new int[lettersPerRow]; // defaults to 0
+                        rowOccupancy[row] = occ;
+                    }
+
+                    // Find the lowest track that can host this span = current max occupancy across span
+                    int trackIndex = 0;
+                    for (int c = thisStartCol; c <= thisEndCol && c < lettersPerRow; c++)
+                        trackIndex = Math.Max(trackIndex, occ[c]);
+
+                    // Reserve that track across the span
+                    for (int c = thisStartCol; c <= thisEndCol && c < lettersPerRow; c++)
+                        occ[c] = trackIndex + 1;
+
+                    // Now draw using this track’s vertical offset
+                    double x = plotMargin + thisStartCol * letterWidth;
+                    double y = plotYOffset
+                               + row * (letterHeight + yPad + rectHeight * 2)
+                               + letterHeight + yPad
+                               + trackIndex * rectJitter;
+                    double width = drawLen * letterWidth;
+                    double height = rectHeight;
+
+                    // Determine which corners to round
+                    double r = 6;
+                    bool roundLeft = false, roundRight = false;
+
+                    if (isFirstSegment)
+                        roundLeft = true;
+                    if (remaining == drawLen)
+                        roundRight = true;
+
+                    // Use a slightly opaque brush for fill
+                    var baseBrush = GetColorBrush(res);
+                    var color = (baseBrush as SolidColorBrush)?.Color ?? Colors.Gray;
+                    var brush = new SolidColorBrush(color) { Opacity = 0.75 };
+                    brush.Freeze();
+
+                    // Create a fully opaque, darkened pen for the outline
+                    Color outlineColor = Color.Multiply(color, 0.9f); // darken for contrast
+                    var outlinePen = new Pen(new SolidColorBrush(outlineColor) { Opacity = 1.0 }, 2.0);
+                    outlinePen.Freeze();
+
+                    if (roundLeft || roundRight)
+                    {
+                        // Custom geometry for per-corner rounding
+                        var geometry = new StreamGeometry();
+                        using (var ctx = geometry.Open())
+                        {
+                            // Top left
+                            if (roundLeft)
+                                ctx.BeginFigure(new Point(x + r, y), true, true);
+                            else
+                                ctx.BeginFigure(new Point(x, y), true, true);
+
+                            // Top edge
+                            ctx.LineTo(new Point(x + width - (roundRight ? r : 0), y), true, false);
+
+                            // Top right
+                            if (roundRight)
+                                ctx.ArcTo(new Point(x + width, y + r), new Size(r, r), 0, false, SweepDirection.Clockwise, true, false);
+                            else
+                                ctx.LineTo(new Point(x + width, y), true, false);
+
+                            // Right edge
+                            ctx.LineTo(new Point(x + width, y + height - (roundRight ? r : 0)), true, false);
+
+                            // Bottom right
+                            if (roundRight)
+                                ctx.ArcTo(new Point(x + width - r, y + height), new Size(r, r), 0, false, SweepDirection.Clockwise, true, false);
+                            else
+                                ctx.LineTo(new Point(x + width, y + height), true, false);
+
+                            // Bottom edge
+                            ctx.LineTo(new Point(x + (roundLeft ? r : 0), y + height), true, false);
+
+                            // Bottom left
+                            if (roundLeft)
+                                ctx.ArcTo(new Point(x, y + height - r), new Size(r, r), 0, false, SweepDirection.Clockwise, true, false);
+                            else
+                                ctx.LineTo(new Point(x, y + height), true, false);
+
+                            // Left edge
+                            ctx.LineTo(new Point(x, y + (roundLeft ? r : 0)), true, false);
+
+                            // Top left
+                            if (roundLeft)
+                                ctx.ArcTo(new Point(x + r, y), new Size(r, r), 0, false, SweepDirection.Clockwise, true, false);
+                            else
+                                ctx.LineTo(new Point(x, y), true, false);
+                        }
+                        geometry.Freeze();
+                        dc.DrawGeometry(brush, outlinePen, geometry);
+                    }
+                    else
+                    {
+                        // No rounded corners, no outline
+                        dc.DrawRectangle(brush, null, new Rect(x, y, width, height));
+                    }
+
+                    remaining -= drawLen;
+                    idx += drawLen;
+                    row++;
+                    col = 0;
+                    isFirstSegment = false;
+                }
+            }
+
+            // --- Draw letters, bold and evenly spaced, with margin ---
+            // Add row index labels on both sides
+            // Draw the letters for this row and determine the vertical alignment
+            for (int row = 0; row < nRows; row++)
+            {
+                int rowStartIdx = row * lettersPerRow;
+                int rowEndIdx = Math.Min(seq.Length, (row + 1) * lettersPerRow) - 1;
+                double y = plotYOffset + row * (letterHeight + yPad + rectHeight * 2);
+
+                // Prepare left/right labels
+                var leftLabelText = (rowStartIdx + 1).ToString();
+                var rightLabelText = (rowEndIdx + 1).ToString();
+                var labelFontSize = Math.Max(6, fontSize - 4);
+
+                var leftLabel = new FormattedText(
+                    leftLabelText,
+                    System.Globalization.CultureInfo.CurrentCulture,
+                    FlowDirection.LeftToRight,
+                    new Typeface("Segoe UI"),
+                    labelFontSize,
+                    Brushes.DimGray,
+                    dpi);
+
+                var rightLabel = new FormattedText(
+                    rightLabelText,
+                    System.Globalization.CultureInfo.CurrentCulture,
+                    FlowDirection.LeftToRight,
+                    new Typeface("Segoe UI"),
+                    labelFontSize,
+                    Brushes.DimGray,
+                    dpi);
+
+                // Use the first letter in the row for vertical alignment
+                int firstIdx = rowStartIdx;
+                var letterText = new FormattedText(
+                    seq[firstIdx].ToString(),
+                    System.Globalization.CultureInfo.CurrentCulture,
+                    FlowDirection.LeftToRight,
+                    new Typeface(new FontFamily("Segoe UI"), FontStyles.Normal, FontWeights.Bold, FontStretches.Normal),
+                    fontSize,
+                    Brushes.Black,
+                    dpi);
+
+                // Align baselines: offset so that the baseline of the label matches the baseline of the letter
+                double baselineOffset = y + letterText.Baseline - leftLabel.Baseline;
+
+                double leftLabelX = plotMargin - leftLabel.Width - 6;
+                double rightLabelX = plotMargin + usableWidth + 6;
+
+                dc.DrawText(leftLabel, new Point(leftLabelX, baselineOffset));
+                dc.DrawText(rightLabel, new Point(rightLabelX, baselineOffset));
+
+                // Draw the letters for this row
+                for (int col = 0; col < lettersPerRow; col++)
+                {
+                    int i = rowStartIdx + col;
+                    if (i >= seq.Length)
+                        break;
+
+                    double x = plotMargin + col * letterWidth;
+                    var formattedText = new FormattedText(
+                        seq[i].ToString(),
+                        System.Globalization.CultureInfo.CurrentCulture,
+                        FlowDirection.LeftToRight,
+                        new Typeface(new FontFamily("Segoe UI"), FontStyles.Normal, FontWeights.Bold, FontStretches.Normal),
+                        fontSize,
+                        Brushes.Black,
+                        dpi);
+
+                    double centeredX = x + (letterWidth - formattedText.Width) / 2;
+                    dc.DrawText(formattedText, new Point(centeredX, y));
+                }
+            }
+        }
+
+        CoverageDrawing = new DrawingImage(dv.Drawing);
+    }
+
+    // Preferred legend order
+    private static readonly BioPolymerCoverageType[] LegendOrder =
+    {
+        BioPolymerCoverageType.Unique,
+        BioPolymerCoverageType.UniqueMissedCleavage,
+        BioPolymerCoverageType.TandemRepeat,
+        BioPolymerCoverageType.TandemRepeatMissedCleavage,
+        BioPolymerCoverageType.Shared,
+        BioPolymerCoverageType.SharedMissedCleavage
+    };
+
+    private List<(SolidColorBrush Brush, FormattedText Text)> CreateLegendItems( List<BioPolymerCoverageResultModel> filteredResults, double fontSize, double dpi, ColorResultsBy colorBy)
+    {
+        var items = new List<(SolidColorBrush, FormattedText)>();
+        if (colorBy == ColorResultsBy.None)
+            return items;
+
+        if (colorBy == ColorResultsBy.FileOrigin)
+        {
+            var countsByFile = filteredResults
+                .GroupBy(r => r.Match.FileName)
+                .ToDictionary(g => g.Key, g => g.Count());
+
+            string unitLabel = filteredResults.FirstOrDefault()?.Match.GetDigestionProductLabel();
+
+            foreach (var kvp in countsByFile)
+            {
+                string fileName = kvp.Key;
+                int count = kvp.Value;
+                if (string.IsNullOrEmpty(fileName) || count == 0) continue;
+
+                string label = $"{fileName} {unitLabel}s: {count}";
+                var ft = new FormattedText(
+                    label,
+                    System.Globalization.CultureInfo.CurrentCulture,
+                    FlowDirection.LeftToRight,
+                    new Typeface("Segoe UI"),
+                    fontSize * 0.8,
+                    Brushes.Black,
+                    dpi);
+                items.Add((GetColorByIdentifier(fileName), ft));
+            }
+            return items;
+        }
+
+        var countsByType = filteredResults.GroupBy(r => r.CoverageType)
+            .ToDictionary(g => g.Key, g => g.Count());
+
+        string unitLabelType = filteredResults.FirstOrDefault()?.Match.GetDigestionProductLabel();
+
+        foreach (var t in LegendOrder)
+        {
+            if (!countsByType.TryGetValue(t, out int count) || count == 0) continue;
+
+            string label = $"{BaseViewModel.AddSpaces(t.ToString())} {unitLabelType}s: {count}";
+            var ft = new FormattedText(
+                label,
+                System.Globalization.CultureInfo.CurrentCulture,
+                FlowDirection.LeftToRight,
+                new Typeface("Segoe UI"),
+                fontSize * 0.8,
+                Brushes.Black,
+                dpi);
+            items.Add((MetaDrawSettings.BioPolymerCoverageColors[t], ft));
+        }
+        return items;
+    }
+
+    // Helper: wrap legend items into lines that fit within usableWidth
+    private List<List<(SolidColorBrush Brush, FormattedText Text)>> WrapLegendItems(
+        List<(SolidColorBrush Brush, FormattedText Text)> items,
+        double fontSize,
+        double usableWidth,
+        double sepWidth)
+    {
+        var lines = new List<List<(SolidColorBrush Brush, FormattedText Text)>>();
+        var currentLine = new List<(SolidColorBrush Brush, FormattedText Text)>();
+        double currentWidth = 0;
+
+        foreach (var item in items)
+        {
+            double itemWidth = fontSize * 0.8 + 6 + item.Text.Width + (currentLine.Count > 0 ? sepWidth : 0);
+            if (currentLine.Count > 0 && currentWidth + itemWidth > usableWidth)
+            {
+                lines.Add(currentLine);
+                currentLine = new List<(SolidColorBrush Brush, FormattedText Text)>();
+                currentWidth = 0;
+                itemWidth = fontSize * 0.8 + 6 + item.Text.Width;
+            }
+            currentLine.Add(item);
+            currentWidth += itemWidth;
+        }
+        if (currentLine.Count > 0)
+            lines.Add(currentLine);
+
+        return lines;
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageResultModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageResultModel.cs
new file mode 100644
index 000000000..bd06f190d
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageResultModel.cs
@@ -0,0 +1,15 @@
+using Readers;
+
+namespace GuiFunctions.MetaDraw;
+
+public class BioPolymerCoverageResultModel(SpectrumMatchFromTsv match, string baseSequence, int start, int end, BioPolymerCoverageType coverageType)
+{
+    public readonly SpectrumMatchFromTsv Match = match;
+    public string BaseSequence { get; } = baseSequence;
+    public int Start { get; } = start;
+    public int End { get; } = end;
+    public BioPolymerCoverageType CoverageType { get; } = coverageType;
+    public double QValue => Match.QValue;
+    public string Ambiguity => Match.AmbiguityLevel;
+    public string FileName => Match.FileName;
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageType.cs b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageType.cs
new file mode 100644
index 000000000..1593d0d30
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerCoverageType.cs
@@ -0,0 +1,11 @@
+namespace GuiFunctions.MetaDraw;
+
+public enum BioPolymerCoverageType
+{
+    Unique,
+    UniqueMissedCleavage,
+    TandemRepeat,               // Shared within the same biopolymer
+    TandemRepeatMissedCleavage,
+    Shared,                     // Shared between different biopolymers
+    SharedMissedCleavage,
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerGroupViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerGroupViewModel.cs
new file mode 100644
index 000000000..df7a392bf
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerGroupViewModel.cs
@@ -0,0 +1,59 @@
+using System;
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.Linq;
+
+namespace GuiFunctions.MetaDraw;
+
+public class BioPolymerGroupViewModel : BaseViewModel
+{
+    public string Accession { get; }
+    public string ProteinName { get; }
+    public string Sequence { get; }
+    public int Length => Sequence.Length;
+    public int GroupCount { get; private set; }
+    public double UniqueSequenceCoverage { get; private set; }
+    public double MaximumSequenceCoverage { get; private set; }
+    public ObservableCollection<BioPolymerCoverageResultModel> CoverageResults { get; }
+
+    public BioPolymerGroupViewModel(string accession, string proteinName, string sequence, IEnumerable<BioPolymerCoverageResultModel> results)
+    {
+        Accession = accession;
+        ProteinName = proteinName;
+        Sequence = sequence;
+        CoverageResults = new(results);
+        UpdatePropertiesAfterFilter();
+    }
+
+    public void UpdatePropertiesAfterFilter()
+    {
+        int count = 0;
+        bool[] uniqueCovered = new bool[Sequence.Length];
+        bool[] maxCovered = new bool[Sequence.Length];
+
+        foreach (var res in CoverageResults.Where(p => MetaDrawSettings.FilterAcceptsPsm(p.Match)))
+        {
+            count++;
+            int start = Math.Max(0, res.Start - 1);
+            int end = Math.Min(Sequence.Length - 1, res.End - 1);
+
+            // Maximum coverage: all results
+            for (int i = start; i <= end; i++)
+                maxCovered[i] = true;
+
+            // Unique coverage: only Unique or UniqueMissedCleavage
+            if (res.CoverageType == BioPolymerCoverageType.Unique || res.CoverageType == BioPolymerCoverageType.UniqueMissedCleavage)
+            {
+                for (int i = start; i <= end; i++)
+                    uniqueCovered[i] = true;
+            }
+        }
+
+        GroupCount = count;
+        UniqueSequenceCoverage = uniqueCovered.Count(b => b) / (double)Sequence.Length;
+        MaximumSequenceCoverage = maxCovered.Count(b => b) / (double)Sequence.Length;
+        OnPropertyChanged(nameof(GroupCount));
+        OnPropertyChanged(nameof(MaximumSequenceCoverage));
+        OnPropertyChanged(nameof(UniqueSequenceCoverage));
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerTabViewModel.cs
new file mode 100644
index 000000000..0e363216a
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/BioPolymerCoverage/BioPolymerTabViewModel.cs
@@ -0,0 +1,381 @@
+using System;
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.Diagnostics.CodeAnalysis;
+using System.IO;
+using System.Linq;
+using System.Threading;
+using System.Threading.Tasks;
+using System.Windows;
+using System.Windows.Data;
+using System.Windows.Input;
+using System.Windows.Media;
+using System.Windows.Media.Imaging;
+using Easy.Common.Extensions;
+using EngineLayer;
+using MzLibUtil;
+using Omics;
+using Readers;
+using TaskLayer;
+using UsefulProteomicsDatabases;
+
+namespace GuiFunctions.MetaDraw;
+
+public class BioPolymerTabViewModel : MetaDrawTabViewModel
+{
+    private Dictionary<string, IBioPolymer> _allBioPolymers;
+    private readonly MetaDrawLogic _metaDrawLogic;
+    public override string TabHeader { get; init; } = "BioPolymer Coverage";
+
+    public BioPolymerTabViewModel(MetaDrawLogic metaDrawLogic, string exportDirectory = null)
+    {
+        IsDatabaseLoaded = false;
+        _metaDrawLogic = metaDrawLogic;
+        _allBioPolymers = new Dictionary<string, IBioPolymer>();
+        AllGroups = new ObservableCollection<BioPolymerGroupViewModel>();
+        DatabasePath = string.Empty;
+        ExportDirectory = exportDirectory ?? Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments);
+
+        LoadDatabaseCommand = new RelayCommand(LoadDatabase);
+        ResetDatabaseCommand = new RelayCommand(ResetDatabase);
+        ExportImageCommand = new RelayCommand(ExportImage);
+
+        BindingOperations.EnableCollectionSynchronization(AllGroups, ThreadLocker);
+        BindingOperations.EnableCollectionSynchronization(FilteredGroups, ThreadLocker);
+    }
+
+    #region Database Loading Handling
+
+    private bool _isDatabaseLoaded;
+
+    public bool IsDatabaseLoaded
+    {
+        get => _isDatabaseLoaded;
+        set
+        {
+            _isDatabaseLoaded = value;
+            OnPropertyChanged(nameof(IsDatabaseLoaded));
+        }
+    }
+
+    private string _databasePath;
+
+    public string DatabasePath
+    {
+        get => _databasePath;
+        set
+        {
+            _databasePath = value;
+            OnPropertyChanged(nameof(DatabasePath));
+            DatabaseName =PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(_databasePath);
+        }
+    }
+
+    private string _databaseName;
+
+    public string DatabaseName
+    {
+        get => _databaseName;
+        set
+        {
+            _databaseName = value;
+            OnPropertyChanged(nameof(DatabaseName));
+        }
+    }
+
+    public ICommand LoadDatabaseCommand { get; set; }
+    public ICommand ResetDatabaseCommand { get; set; }
+
+    private async void LoadDatabase()
+    {
+        if (string.IsNullOrWhiteSpace(DatabasePath))
+            return;
+
+        IsLoading = true;
+        try
+        {
+            // Load biopolymers asynchronously
+            var bioPolymers = await Task.Run(() =>
+                new SearchTask().LoadBioPolymers(
+                    "", new() { new DbForTask(DatabasePath, false) }, true, DecoyType.None, new(), new())
+                .ToDictionary(p => p.Accession, p => p)
+            );
+
+            _allBioPolymers = bioPolymers;
+
+            if (_allBioPolymers.Count == 0)
+            {
+                MessageBoxHelper.Warn($"No {GlobalVariables.AnalyteType.GetBioPolymerLabel()} loaded from database.");
+                return;
+            }
+
+            IsDatabaseLoaded = true;
+
+            if (_metaDrawLogic.AllSpectralMatches is { Count: > 0 })
+            {
+                try
+                {
+                    ProcessSpectralMatches(_metaDrawLogic.AllSpectralMatches);
+                }
+                catch (Exception ex) { MessageBoxHelper.Warn($"Error processing spectral matches: {ex.Message}"); }
+            }
+
+            if (AllGroups.Count == 0)
+            {
+                MessageBoxHelper.Warn($"Database loaded, but no {GlobalVariables.AnalyteType.GetSpectralMatchLabel()}s matched by accession.");
+            }
+        }
+        catch (Exception e) { MessageBoxHelper.Warn($"An error occurred while loading the database:\n{e}"); }
+        finally
+        {
+            IsLoading = false;
+        }
+    }
+
+    private void ResetDatabase()
+    {
+        DatabasePath = string.Empty;
+        DatabaseName = string.Empty;
+        _allBioPolymers.Clear();
+        AllGroups.Clear();
+        FilteredGroups.Clear();
+    }
+
+    #endregion
+
+    private string _searchText;
+    public string SearchText
+    {
+        get => _searchText;
+        set
+        {
+            if (_searchText != value)
+            {
+                _searchText = value;
+                OnPropertyChanged(nameof(SearchText));
+                UpdateFilteredGroups();
+            }
+        }
+    }
+
+    public ObservableCollection<BioPolymerGroupViewModel> FilteredGroups { get; } = new();
+
+    public ObservableCollection<BioPolymerGroupViewModel> AllGroups { get; set; }
+    public BioPolymerCoverageMapViewModel CoverageMapViewModel { get; } = new();
+
+    private BioPolymerGroupViewModel _selectedGroup;
+    public BioPolymerGroupViewModel SelectedGroup
+    {
+        get => _selectedGroup;
+        set
+        {
+            _selectedGroup = value;
+            OnPropertyChanged(nameof(SelectedGroup));
+            CoverageMapViewModel.Group = value;
+        }
+    }
+
+    public void ProcessSpectralMatches(IList<SpectrumMatchFromTsv> matches, CancellationToken cancellationToken = default)
+    {
+        AllGroups.Clear();
+
+        // Build a mapping: accession => list of best matches for that accession
+        var bestMatchesBySequence = matches
+            .GroupBy(p => p.BaseSequence)
+            .Select(group => group.MinBy(sm => sm.QValue))
+            .ToList();
+
+        // Map: accession => List<SpectrumMatchFromTsv>
+        var accessionToMatches = new Dictionary<string, List<SpectrumMatchFromTsv>>();
+
+        foreach (var match in bestMatchesBySequence)
+        {
+            foreach (var acc in match.Accession.Split('|'))
+            {
+                if (!accessionToMatches.TryGetValue(acc, out var list))
+                {
+                    list = new List<SpectrumMatchFromTsv>();
+                    accessionToMatches[acc] = list;
+                }
+                list.Add(match);
+            }
+        }
+
+        var processedResults = new List<BioPolymerCoverageResultModel>();
+        foreach (var accessionToGroup in accessionToMatches.Keys)
+        {
+            if (cancellationToken.IsCancellationRequested)
+                throw new OperationCanceledException();
+
+            if (!_allBioPolymers.TryGetValue(accessionToGroup, out var bioPolymer))
+                continue;
+
+            var relevantMatches = accessionToMatches[accessionToGroup];
+            processedResults.Clear();
+
+            foreach (var match in relevantMatches)
+            {
+                BioPolymerCoverageType covType;
+
+                var accessionSplits = match.Accession.Split("|");
+                var siteSplits = match.GetStartAndEndPosition().ToArray();
+                bool singleAccession = accessionSplits.Length == 1;
+                bool singleLocalization = siteSplits.Length == 1;
+
+                // TODO: Better ambiguity handling for missed cleavages. 
+                var missedCleavageSplits = match.MissedCleavage?.Split("|").Select(int.Parse).ToArray() ?? new int[] { 0 };
+                int missedCleavages = missedCleavageSplits[0];
+
+                // belongs to single biopolymer and single localization 
+                if (singleAccession && singleLocalization)
+                {
+                    if (missedCleavages == 0)
+                        covType = BioPolymerCoverageType.Unique;
+                    else
+                        covType = BioPolymerCoverageType.UniqueMissedCleavage;
+
+                    processedResults.Add(new(match, match.BaseSeq, siteSplits[0].Start, siteSplits[0].End, covType));
+                }
+                // belongs to multiple biopolymers
+                else if (accessionSplits.Length == siteSplits.Length) 
+                {
+                    int relevantIndex = accessionSplits.IndexOf(accessionToGroup);
+
+                    if (missedCleavages == 0)
+                        covType = BioPolymerCoverageType.Shared;
+                    else
+                        covType = BioPolymerCoverageType.SharedMissedCleavage;
+
+                    processedResults.Add(new(match, match.BaseSeq, siteSplits[relevantIndex].Start, siteSplits[relevantIndex].End, covType));
+                }
+                // belongs to multiple biopolymers but shares same localization
+                else if (!singleAccession && singleLocalization)
+                {
+                    if (missedCleavages == 0)
+                        covType = BioPolymerCoverageType.Shared;
+                    else
+                        covType = BioPolymerCoverageType.SharedMissedCleavage;
+
+                    processedResults.Add(new(match, match.BaseSeq, siteSplits[0].Start, siteSplits[0].End, covType));
+                }
+                // belongs to single biopolymer with multiple localizations
+                else if (singleAccession) 
+                {
+                    if (missedCleavages == 0)
+                        covType = BioPolymerCoverageType.TandemRepeat;
+                    else
+                        covType = BioPolymerCoverageType.TandemRepeatMissedCleavage;
+
+                    for (int i = 0; i < siteSplits.Length; i++)
+                    {
+                        processedResults.Add(new(match, match.BaseSeq, siteSplits[i].Start, siteSplits[i].End, covType));
+                    }
+                }
+                // Mismatch b/n accessions and start/end indexes. This occurs when one of the fields does not have a distinct value (e.g. peptide is in 3 protein sequences but has the same start and end in two of the sequences). 
+                else
+                {
+                    var startIndicesInBioPolymer = bioPolymer.BaseSequence.IndexOfAll(match.BaseSeq)
+                        .Select(p => p + 1)
+                        .ToArray();
+                    foreach (var potentialSite in siteSplits)
+                    {
+                        if (startIndicesInBioPolymer.Contains(potentialSite.Start))
+                        {
+                            // Found a match
+                            if (missedCleavages == 0)
+                                covType = BioPolymerCoverageType.Shared;
+                            else
+                                covType = BioPolymerCoverageType.SharedMissedCleavage;
+                            processedResults.Add(new(match, match.BaseSeq, potentialSite.Start, potentialSite.End, covType));
+                        }
+                    }
+                }
+            }
+
+            if (processedResults.Count == 0)
+                continue;
+
+            var group = new BioPolymerGroupViewModel(accessionToGroup, bioPolymer.Name, bioPolymer.BaseSequence, processedResults);
+            AllGroups.Add(group);
+        }
+
+        UpdateFilteredGroups();
+    }
+
+    private void UpdateFilteredGroups()
+    {
+        FilteredGroups.Clear();
+        var query = string.IsNullOrWhiteSpace(SearchText)
+            ? AllGroups
+            : AllGroups.Where(g =>
+                (g.Accession?.IndexOf(SearchText, StringComparison.OrdinalIgnoreCase) >= 0) ||
+                (g.ProteinName?.IndexOf(SearchText, StringComparison.OrdinalIgnoreCase) >= 0));
+        foreach (var group in query.OrderByDescending(p => p.UniqueSequenceCoverage).ThenByDescending(p => p.MaximumSequenceCoverage))
+            FilteredGroups.Add(group);
+    }
+
+    #region Image Export
+
+    public ICommand ExportImageCommand { get; set; }
+
+    private void ExportImage()
+    {
+        // Get the DrawingImage from the CoverageMapViewModel
+        var drawingImage = CoverageMapViewModel.CoverageDrawing;
+        if (drawingImage == null)
+            return;
+
+        // Use the DrawingImage's dimensions for export
+        double width = 800;
+        double height = 480;
+        if (drawingImage.Drawing != null)
+        {
+            Rect bounds = drawingImage.Drawing.Bounds;
+            if (!bounds.IsEmpty && bounds.Width > 0 && bounds.Height > 0)
+            {
+                width = bounds.Width;
+                height = bounds.Height;
+            }
+        }
+
+        var drawingVisual = new DrawingVisual();
+        using (var dc = drawingVisual.RenderOpen())
+        {
+            dc.DrawImage(drawingImage, new Rect(0, 0, width, height));
+        }
+
+        // Use MetaDrawSettings.CanvasPdfExportDpi for DPI
+        double dpi = MetaDrawSettings.CanvasPdfExportDpi;
+        var rtb = new RenderTargetBitmap(
+            (int)Math.Ceiling(width * dpi / 96.0),
+            (int)Math.Ceiling(height * dpi / 96.0),
+            dpi, dpi, PixelFormats.Pbgra32);
+        rtb.Render(drawingVisual);
+
+        string path = Path.Combine(ExportDirectory, $"{SelectedGroup.Accession}_SequenceCoverage.{MetaDrawSettings.ExportType.ToLower()}");
+
+        // Convert RenderTargetBitmap to System.Drawing.Bitmap
+        using (var ms = new MemoryStream())
+        {
+            var encoder = new PngBitmapEncoder();
+            encoder.Frames.Add(BitmapFrame.Create(rtb));
+            encoder.Save(ms);
+            ms.Seek(0, SeekOrigin.Begin);
+            using (var bmp = new System.Drawing.Bitmap(ms))
+            {
+                MetaDrawLogic.ExportBitmap(bmp, path);
+            }
+        }
+
+        MessageBoxHelper.Show($"Exported Coverage Plot to {path}");
+    }
+
+    #endregion
+}
+
+
+[ExcludeFromCodeCoverage]
+public class BioPolymerTabModel() : BioPolymerTabViewModel(new())
+{
+    public static BioPolymerTabModel Instance => new();
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/ChimeraAnalysisTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/ChimeraAnalysisTabViewModel.cs
index 7a7924e54..e70ed57e0 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/ChimeraAnalysisTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/ChimeraAnalysisTabViewModel.cs
@@ -12,18 +12,22 @@
 using System.Windows.Media;
 using Easy.Common.Extensions;
 using Point = System.Windows.Point;
+using System.Windows.Data;
+using System.Threading;
 
 namespace GuiFunctions.MetaDraw;
 
 /// <summary>
 /// All data and user triggered manipulations for the Chimera Analysis tab
 /// </summary>
-public class ChimeraAnalysisTabViewModel : BaseViewModel
+public class ChimeraAnalysisTabViewModel : MetaDrawTabViewModel
 {
     #region Displayed in GUI
+    public override string TabHeader { get; init; } = "Chimera Annotation";
     public ChimeraSpectrumMatchPlot ChimeraSpectrumMatchPlot { get; set; }
     public Ms1ChimeraPlot Ms1ChimeraPlot { get; set; }
     public ObservableCollection<ChimeraGroupViewModel> ChimeraGroupViewModels { get; set; }
+    public Dictionary<string, MsDataFile> MsDataFiles { get; private set; }
 
     private ChimeraGroupViewModel _selectedChimeraGroup;
     public ChimeraGroupViewModel SelectedChimeraGroup
@@ -80,23 +84,34 @@ public bool UseLetterOnly
     }
 
     #endregion
-
-    public ChimeraAnalysisTabViewModel(List<SpectrumMatchFromTsv> allPsms, Dictionary<string, MsDataFile> dataFiles, string exportDirectory = null)
+    public ChimeraAnalysisTabViewModel(string exportDirectory = null)
     {
-        ChimeraGroupViewModels = [..ConstructChimericPsms(allPsms, dataFiles)
-            .OrderByDescending(p => p.Count)
-            .ThenByDescending(p => p.UniqueFragments)
-            .ThenByDescending(p => p.TotalFragments)];
+        ChimeraGroupViewModels = new();
         ExportDirectory = exportDirectory ?? Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments);
-
         ExportMs1Command = new RelayCommand(ExportMs1);
         ExportMs2Command = new RelayCommand(ExportMs2);
         ExportSequenceCoverageCommand = new RelayCommand(ExportSequenceCoverage);
         ExportLegendCommand = new DelegateCommand(ExportLegend);
         ExportAllCommand = new DelegateCommand(ExportAll);
+
+        BindingOperations.EnableCollectionSynchronization(ChimeraGroupViewModels, ThreadLocker);
+    }
+
+    public void ProcessChimeraData(List<SpectrumMatchFromTsv> allPsms, Dictionary<string, MsDataFile> dataFiles, CancellationToken cancellationToken = default)
+    {
+        MsDataFiles = dataFiles;
+        ChimeraGroupViewModels.Clear();
+
+        foreach (var chimeraGroup in ConstructChimericPsms(allPsms, dataFiles, cancellationToken)
+                     .OrderByDescending(p => p.Count)
+                     .ThenByDescending(p => p.UniqueFragments)
+                     .ThenByDescending(p => p.TotalFragments))
+        {
+            ChimeraGroupViewModels.Add(chimeraGroup);
+        }
     }
 
-    public static List<ChimeraGroupViewModel> ConstructChimericPsms(List<SpectrumMatchFromTsv> psms, Dictionary<string, MsDataFile> dataFiles)
+    public static List<ChimeraGroupViewModel> ConstructChimericPsms(List<SpectrumMatchFromTsv> psms, Dictionary<string, MsDataFile> dataFiles, CancellationToken cancellationToken = default)
     {
         // Groups are made from psms that pass the MetaDraw quality filter and only include decoys if we are showing decoys.
         var filteredPsms = new List<SpectrumMatchFromTsv>(psms.Count);
@@ -116,6 +131,9 @@ public static List<ChimeraGroupViewModel> ConstructChimericPsms(List<SpectrumMat
         List<ChimeraGroupViewModel> toReturn = new(groupDict.Count);
         foreach (var group in groupDict.Values)
         {
+            if (cancellationToken.IsCancellationRequested)
+                throw new OperationCanceledException();
+
             if (group.Count <= 1)
                 continue;
 
@@ -134,7 +152,7 @@ public static List<ChimeraGroupViewModel> ConstructChimericPsms(List<SpectrumMat
             // This prevents the program from crashing and skips problematic groups.
             try
             {
-                var orderedGroup = group.OrderByDescending(p => p.Score);
+                var orderedGroup = group.OrderByDescending(p => p.Score); 
                 var groupVm = new ChimeraGroupViewModel(orderedGroup, ms1Scan, ms2Scan);
                 if (groupVm.ChimericPsms.Count > 0)
                     toReturn.Add(groupVm);
@@ -150,22 +168,6 @@ public static List<ChimeraGroupViewModel> ConstructChimericPsms(List<SpectrumMat
 
     #region IO
 
-    private string _exportDirectory;
-    public string ExportDirectory
-    {
-        get
-        {
-            if (!Directory.Exists(_exportDirectory))
-                Directory.CreateDirectory(_exportDirectory);
-            return _exportDirectory;
-        }
-        set
-        {
-            _exportDirectory = value;
-            OnPropertyChanged(nameof(ExportDirectory));
-        }
-    }
-
     public ICommand ExportMs1Command { get; set; }
     public ICommand ExportMs2Command { get; set; }
     public ICommand ExportSequenceCoverageCommand { get; set; }
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/ChimeraLegendCanvas.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/ChimeraLegendCanvas.cs
index 81e4546ce..cc4019c29 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/ChimeraLegendCanvas.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/ChimeraLegendCanvas.cs
@@ -174,7 +174,7 @@ private void BuildLegend()
         double leftMargin = 10;
         double ellipseAndSpacing = 18;
         double rightMargin = 10;
-        Width = leftMargin + ellipseAndSpacing + maxTextWidth + rightMargin;
+        Width = Math.Min(leftMargin + ellipseAndSpacing + maxTextWidth + rightMargin, MetaDrawSettings.ChimeraLegendMaxWidth);
         Height = y + 10;
     }
 
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MetaDrawTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MetaDrawTabViewModel.cs
new file mode 100644
index 000000000..ddb6f3bdd
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MetaDrawTabViewModel.cs
@@ -0,0 +1,50 @@
+using System.IO;
+
+namespace GuiFunctions.MetaDraw;
+
+public abstract class MetaDrawTabViewModel : BaseViewModel
+{
+    protected MetaDrawTabViewModel(bool isTabEnabled = true)
+    {
+        IsTabEnabled = isTabEnabled;
+    }
+
+    protected object ThreadLocker { get; } = new();
+    public abstract string TabHeader { get; init; }
+
+    // Used when tab is loading externally to disable the tab (from MetaDrawDataLoader)
+    private bool _isTabEnabled;
+    public bool IsTabEnabled
+    {
+        get => _isTabEnabled;
+        set { _isTabEnabled = value; OnPropertyChanged(nameof(IsTabEnabled)); }
+    }
+
+    private string _exportDirectory;
+    public string ExportDirectory
+    {
+        get
+        {
+            if (!Directory.Exists(_exportDirectory))
+                Directory.CreateDirectory(_exportDirectory);
+            return _exportDirectory;
+        }
+        set
+        {
+            _exportDirectory = value;
+            OnPropertyChanged(nameof(ExportDirectory));
+        }
+    }
+
+    // Used when the tab is loading internally (adding a database or loading a file)
+    private bool _isLoading;
+    public bool IsLoading
+    {
+        get => _isLoading;
+        set
+        {
+            _isLoading = value;
+            OnPropertyChanged(nameof(IsLoading));
+        }
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/Ms1ChimeraPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/Ms1ChimeraPlot.cs
index 14cf9d4f4..7d942af59 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/Ms1ChimeraPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/Ms1ChimeraPlot.cs
@@ -1,10 +1,5 @@
-using System.Collections.Generic;
-using System.Linq;
-using MzLibUtil;
-using Omics.Fragmentation;
-using OxyPlot;
+using MzLibUtil;
 using OxyPlot.Wpf;
-using LineSeries = OxyPlot.Series.LineSeries;
 
 namespace GuiFunctions.MetaDraw;
 
@@ -21,30 +16,10 @@ public Ms1ChimeraPlot(PlotView plotView, ChimeraGroupViewModel chimeraGroupVm) :
 
         ZoomAxes();
         AnnotateChimericPeaks(chimeraGroupVm);
-        AnnotateIsolationWindow();
+        AnnotateIsolationWindow(Range);
         RefreshChart();
     }
 
-    private void AnnotateIsolationWindow()
-    {
-        var isolationWindow = ChimeraGroup.Ms2Scan.IsolationRange;
-        var yMax = Model.Axes[1].AbsoluteMaximum;
-        var points = new DataPoint[]
-        {
-            new(isolationWindow.Minimum, yMax),
-            new(isolationWindow.Minimum, 0),
-            new(isolationWindow.Maximum, 0),
-            new(isolationWindow.Maximum, yMax),
-        };
-        var lineSeries = new LineSeries
-        {
-            LineStyle = LineStyle.Dash,
-            Color = OxyColors.Red
-        };
-        lineSeries.Points.AddRange(points);
-        Model.Series.Add(lineSeries);
-    }
-
     private void AnnotateChimericPeaks(ChimeraGroupViewModel chimeraGroupVm)
     {
         foreach (var ionGroup in chimeraGroupVm.PrecursorIonsByColor)
@@ -60,9 +35,6 @@ private void AnnotateChimericPeaks(ChimeraGroupViewModel chimeraGroupVm)
 
     public void ZoomAxes()
     {
-        Model.Axes[0].MajorStep = 1;
-        Model.Axes[0].MinorStep = 0.2;
-
         var extracted = ChimeraGroup.Ms1Scan.MassSpectrum.Extract(Range);
         double maxIntensity = 0;
         foreach (var p in extracted)
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconExplorationTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconExplorationTabViewModel.cs
new file mode 100644
index 000000000..68c4caa07
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconExplorationTabViewModel.cs
@@ -0,0 +1,255 @@
+#nullable enable
+using EngineLayer;
+using GuiFunctions.MetaDraw;
+using MassSpectrometry;
+using MathNet.Numerics;
+using MzLibUtil;
+using OxyPlot.Wpf;
+using System;
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.Diagnostics.CodeAnalysis;
+using System.IO;
+using System.Linq;
+using System.Threading;
+using System.Threading.Tasks;
+using System.Windows.Data;
+using System.Windows.Input;
+using ThermoFisher.CommonCore.Data.Business;
+
+namespace GuiFunctions;
+
+public enum DeconvolutionMode
+{
+    FullSpectrum,
+    IsolationRegion
+}
+
+public class DeconExplorationTabViewModel : MetaDrawTabViewModel
+{
+    private readonly MetaDrawLogic _metaDrawLogic;
+    private readonly SemaphoreSlim _populateScansSemaphore = new(1, 1);
+
+    public override string TabHeader { get; init; } = "Deconvolution Exploration";
+    public ObservableCollection<MsDataFile> MsDataFiles { get; set; } = new();
+    public ObservableCollection<MsDataScan> Scans { get; set; } = new();
+    public ObservableCollection<DeconvolutedSpeciesViewModel> DeconvolutedSpecies { get; set; } = new();
+    public DeconvolutionPlot? Plot { get; set; }
+    public List<DeconvolutionMode> DeconvolutionModes { get; } = System.Enum.GetValues<DeconvolutionMode>().ToList();
+
+    private DeconHostViewModel _deconHostViewModel = new();
+    public DeconHostViewModel DeconHostViewModel
+    {
+        get => _deconHostViewModel;
+        set
+        {
+            _deconHostViewModel = value;
+            OnPropertyChanged(nameof(DeconHostViewModel));
+        }
+    }
+
+    private MsDataFile? _selectedMsDataFile;
+    public MsDataFile? SelectedMsDataFile
+    {
+        get => _selectedMsDataFile;
+        set
+        {
+            if (_selectedMsDataFile == value) return;
+            _selectedMsDataFile = value;
+
+            _ = PopulateScansCollection();
+            OnPropertyChanged(nameof(SelectedMsDataFile));
+        }
+    }
+
+    private MsDataScan? _selectedMsDataScan;
+    public MsDataScan? SelectedMsDataScan
+    {
+        get => _selectedMsDataScan;
+        set
+        {
+            if (_selectedMsDataScan == value) return;
+            _selectedMsDataScan = value;
+            OnPropertyChanged(nameof(SelectedMsDataScan));
+        }
+    }
+
+    private DeconvolutionMode _mode = DeconvolutionMode.IsolationRegion;
+    public DeconvolutionMode Mode
+    {
+        get => _mode;
+        set
+        {
+            if (_mode == value) return;
+            _mode = value;
+
+            _ = PopulateScansCollection();
+            OnPropertyChanged(nameof(Mode));
+        }
+    }
+
+    private bool _onlyIdentifiedScans;
+    public bool OnlyIdentifiedScans
+    {
+        get => _onlyIdentifiedScans;
+        set
+        {
+            if (_onlyIdentifiedScans == value) return;
+            _onlyIdentifiedScans = value;
+
+            _ = PopulateScansCollection();
+            OnPropertyChanged(nameof(OnlyIdentifiedScans));
+        }
+    }
+
+    private double minMzToPlot;
+    public double MinMzToPlot
+    {
+        get => minMzToPlot;
+        set
+        {
+            minMzToPlot = value;
+            OnPropertyChanged(nameof(MinMzToPlot));
+        }
+    }
+    private double maxMzToPlot;
+    public double MaxMzToPlot
+    {
+        get => maxMzToPlot;
+        set
+        {
+            maxMzToPlot = value;
+            OnPropertyChanged(nameof(MaxMzToPlot));
+        }
+    }
+
+    public ICommand RunDeconvolutionCommand { get; }
+
+    public DeconExplorationTabViewModel(MetaDrawLogic? metaDrawLogic)
+    {
+        RunDeconvolutionCommand = new DelegateCommand(pv => RunDeconvolution((pv as PlotView)!));
+
+        BindingOperations.EnableCollectionSynchronization(MsDataFiles, ThreadLocker);
+        BindingOperations.EnableCollectionSynchronization(Scans, ThreadLocker);
+        _metaDrawLogic = metaDrawLogic;
+    }
+
+    private void RunDeconvolution(PlotView plotView)
+    {
+        DeconvolutedSpecies.Clear();
+        if (SelectedMsDataScan == null) return;
+
+        IEnumerable<DeconvolutedSpeciesViewModel> results;
+        MzRange? isolationRange;
+        MsDataScan scanToPlot;
+
+        if (Mode == DeconvolutionMode.FullSpectrum)
+        {
+            var min = MinMzToPlot > 0 ? MinMzToPlot : SelectedMsDataScan.MassSpectrum.Range.Minimum;
+            var max = MaxMzToPlot > 0 ? MaxMzToPlot : SelectedMsDataScan.MassSpectrum.Range.Maximum;
+            isolationRange = new MzRange(min, max);
+
+            scanToPlot = SelectedMsDataScan;
+            results = DeconvoluteFullSpectrum(scanToPlot);
+        }
+        else
+        {
+            isolationRange = SelectedMsDataScan.IsolationRange;
+            scanToPlot = SelectedMsDataFile!.GetOneBasedScan(SelectedMsDataScan.OneBasedPrecursorScanNumber!.Value);
+            results = DeconvoluteIsolationRegion(SelectedMsDataScan, scanToPlot);
+        }
+
+        var sortedSpecies = results
+            .Where(p => isolationRange is null || p.Envelope.Peaks.Any(peak => isolationRange.Contains(peak.mz)))
+            .OrderByDescending(p => p.MonoisotopicMass.Round(2))
+            .ThenByDescending(p => p.Charge)
+            .ToList();
+
+        foreach (var species in sortedSpecies)
+            DeconvolutedSpecies.Add(species);
+
+        Plot = new DeconvolutionPlot(plotView, scanToPlot, sortedSpecies, Mode, isolationRange);
+    }
+
+    private IEnumerable<DeconvolutedSpeciesViewModel> DeconvoluteFullSpectrum(MsDataScan scan) 
+        => Deconvoluter.Deconvolute(scan, scan.MsnOrder == 1 ? DeconHostViewModel.PrecursorDeconvolutionParameters.Parameters : DeconHostViewModel.ProductDeconvolutionParameters.Parameters)
+        .Select(envelope => new DeconvolutedSpeciesViewModel(envelope));
+
+    private IEnumerable<DeconvolutedSpeciesViewModel> DeconvoluteIsolationRegion(MsDataScan scan, MsDataScan precursorScan) 
+        => scan.GetIsolatedMassesAndCharges(precursorScan, DeconHostViewModel.PrecursorDeconvolutionParameters.Parameters)
+        .Select(envelope => new DeconvolutedSpeciesViewModel(envelope));
+
+    private async Task PopulateScansCollection()
+    {
+        await _populateScansSemaphore.WaitAsync();
+        try
+        {
+            Scans.Clear();
+
+            if (SelectedMsDataFile == null)
+                return;
+
+            IsLoading = true;
+            try
+            {
+                var selectedMsDataFile = SelectedMsDataFile;
+                var mode = _mode;
+                var onlyIdentifiedScans = OnlyIdentifiedScans;
+                var metaDrawLogic = _metaDrawLogic;
+
+                // Run scan filtering on a background thread
+                var scansToDisplay = await Task.Run(() =>
+                {
+                    IEnumerable<MsDataScan> scans = mode switch
+                    {
+                        DeconvolutionMode.IsolationRegion => selectedMsDataFile.GetMsDataScans().Where(scan => scan.MsnOrder == 2),
+                        DeconvolutionMode.FullSpectrum => selectedMsDataFile.GetMsDataScans(),
+                        _ => Enumerable.Empty<MsDataScan>()
+                    };
+
+                    if (onlyIdentifiedScans)
+                    {
+                        var key = Path.GetFileName(selectedMsDataFile.FilePath.Replace(GlobalVariables.GetFileExtension(selectedMsDataFile.FilePath), string.Empty));
+                        if (metaDrawLogic.SpectralMatchesGroupedByFile.TryGetValue(key, out var matches))
+                        {
+                            HashSet<int> scanNumbers;
+                            if (mode == DeconvolutionMode.FullSpectrum)
+                            {
+                                scanNumbers = matches.Select(m => m.Ms2ScanNumber)
+                                    .Concat(matches.Select(m => m.PrecursorScanNum))
+                                    .ToHashSet();
+                            }
+                            else
+                            {
+                                scanNumbers = matches.Select(m => m.Ms2ScanNumber)
+                                    .ToHashSet();
+                            }
+                            scans = scans.Where(scan => scanNumbers.Contains(scan.OneBasedScanNumber));
+                        }
+                    }
+
+                    return scans;
+                });
+
+                foreach (var scan in scansToDisplay)
+                    Scans.Add(scan);
+            }
+            catch (Exception e) { MessageBoxHelper.Warn($"An error occurred while populating the scan collection:\n{e}"); }
+            finally
+            {
+                IsLoading = false;
+            }
+        }
+        finally
+        {
+            _populateScansSemaphore.Release();
+        }
+    }
+}
+
+
+[ExcludeFromCodeCoverage] // for design time display
+public class DeconTabModel() : DeconExplorationTabViewModel(new MetaDrawLogic())
+{
+    public static DeconTabModel Instance => new();
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconvolutedSpeciesViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconvolutedSpeciesViewModel.cs
new file mode 100644
index 000000000..b021c0966
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconvolutedSpeciesViewModel.cs
@@ -0,0 +1,25 @@
+#nullable enable
+using System.Linq;
+using Chemistry;
+using MassSpectrometry;
+using MathNet.Numerics;
+using OxyPlot;
+
+namespace GuiFunctions;
+
+/// <summary>
+/// Represents a deconvoluted species for visualization. No need to cache results as each property is only called once with current implementation. 
+/// </summary>
+public class DeconvolutedSpeciesViewModel(IsotopicEnvelope envelope) : BaseViewModel
+{
+    public IsotopicEnvelope Envelope { get; } = envelope;
+    public OxyColor Color { get; set; } = OxyColors.Automatic;
+    public double MonoisotopicMass => Envelope.MonoisotopicMass;
+    public int Charge => Envelope.Charge;
+    public int PeakCount => Envelope.Peaks.Count;
+    public double Intensity => Envelope.Peaks.Sum(p => p.intensity);
+    public string Annotation => $"M={MonoisotopicMass.Round(2)}\nz={Charge}";
+    public double MostAbundantMz => Envelope.Peaks.MaxBy(p => p.intensity).mz;
+    public double MonoMz => Envelope.MonoisotopicMass.ToMz(Envelope.Charge);
+    public string PeakMzs => string.Join(", ", Envelope.Peaks.Select(p => p.mz.Round(2)).OrderBy(p => p));
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconvolutionPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconvolutionPlot.cs
new file mode 100644
index 000000000..fad5018ee
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/DeconExploration/DeconvolutionPlot.cs
@@ -0,0 +1,110 @@
+#nullable enable
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using GuiFunctions.Util;
+using MassSpectrometry;
+using MzLibUtil;
+using OxyPlot;
+using OxyPlot.Wpf;
+using FontWeights = OxyPlot.FontWeights;
+using HorizontalAlignment = OxyPlot.HorizontalAlignment;
+using TextAnnotation = OxyPlot.Annotations.TextAnnotation;
+using VerticalAlignment = OxyPlot.VerticalAlignment;
+
+namespace GuiFunctions;
+
+public class DeconvolutionPlot : MassSpectrumPlot
+{
+    public static readonly CyclicalQueue<OxyColor> ColorQueue = new CyclicalQueue<OxyColor>(new[]
+    {
+        OxyColors.Red, OxyColors.Blue, OxyColors.Green, OxyColors.Orange, OxyColors.Purple,
+        OxyColors.Teal, OxyColors.Brown, OxyColors.Pink, OxyColors.Yellow, OxyColors.Gray,
+        OxyColors.Cyan, OxyColors.Magenta, OxyColors.LimeGreen, OxyColors.DarkBlue, OxyColors.DarkRed,
+        OxyColors.DarkGreen, OxyColors.Gold, OxyColors.Indigo, OxyColors.Olive, OxyColors.Maroon,
+        OxyColors.Navy, OxyColors.Turquoise, OxyColors.Violet, OxyColors.Sienna, OxyColors.Salmon,
+        OxyColors.Coral, OxyColors.Khaki, OxyColors.Plum, OxyColors.Peru, OxyColors.SteelBlue,
+        OxyColors.MediumPurple, OxyColors.MediumSeaGreen, OxyColors.MediumSlateBlue, OxyColors.MediumVioletRed,
+        OxyColors.MediumOrchid, OxyColors.MediumTurquoise, OxyColors.MediumSpringGreen, OxyColors.MediumAquamarine
+    });
+
+    public DeconvolutionPlot(PlotView plotView, MsDataScan scan, List<DeconvolutedSpeciesViewModel> deconResults, DeconvolutionMode mode, MzRange? isolationRange = null) : base(plotView, scan)
+    {
+        double maxAnnotated = deconResults.Any()
+            ? deconResults.Max(p => p.Envelope.Peaks.Max(m => m.mz))
+            : isolationRange?.Maximum + 1 ?? scan.MassSpectrum.Range.Maximum;
+
+        double maxIntensity;
+        if (isolationRange != null)
+            maxIntensity = scan.MassSpectrum.Extract(isolationRange).Max(p => p.Intensity);
+        else
+            maxIntensity = scan.MassSpectrum.YofPeakWithHighestY ?? 0;
+
+        ZoomAxes(scan, maxAnnotated, maxIntensity, mode, isolationRange);
+
+        AnnotatePlot(deconResults);
+
+        if (isolationRange is not null && mode == DeconvolutionMode.IsolationRegion)
+            AnnotateIsolationWindow(isolationRange);
+        RefreshChart();
+    }
+
+    public void AnnotatePlot(List<DeconvolutedSpeciesViewModel> deconResults)
+    {
+        if (deconResults is null || deconResults.Count == 0)
+            return;
+
+        for (var index = 0; index < deconResults.Count; index++)
+        {
+            var species = deconResults[index];
+            species.Color = ColorQueue.Dequeue();
+            TextAnnotation annotation = null;
+            foreach (var peak in species.Envelope.Peaks)
+            {
+                int i = Scan.MassSpectrum.GetClosestPeakIndex(peak.mz);
+                double mz = Scan.MassSpectrum.XArray[i];
+                double intensity = Scan.MassSpectrum.YArray[i];
+
+                if (Math.Abs(peak.mz - species.MostAbundantMz) < 1e-6 && MetaDrawSettings.DisplayIonAnnotations)
+                {
+                    annotation = new TextAnnotation
+                    {
+                        Text = species.Annotation,
+                        TextColor = species.Color,
+                        FontSize = MetaDrawSettings.AnnotatedFontSize,
+                        FontWeight = MetaDrawSettings.AnnotationBold ? FontWeights.Bold : 2.0,
+                        TextPosition = new DataPoint(mz, intensity),
+                        TextVerticalAlignment = intensity < 0 ? VerticalAlignment.Top : VerticalAlignment.Bottom,
+                        TextHorizontalAlignment = HorizontalAlignment.Center,
+                        StrokeThickness = 0,
+                    };
+                }
+                DrawPeak(mz, intensity, MetaDrawSettings.StrokeThicknessAnnotated, species.Color, annotation);
+            }
+        }
+    }
+
+    private const double YRangeMultiplier = 1.2;
+    public void ZoomAxes(MsDataScan scan, double maxAnnotatedMz, double maxAnnotatedIntensity, DeconvolutionMode mode, MzRange? isolationRange = null)
+    {
+        Model.Title = $"Scan {scan.OneBasedScanNumber} (MS{scan.MsnOrder})";
+
+        // Full Scan
+        if (mode is DeconvolutionMode.FullSpectrum)
+        {
+            var max = isolationRange?.Maximum ?? maxAnnotatedMz + 50;
+            var min = isolationRange?.Minimum ?? scan.MassSpectrum.Range.Minimum;
+
+            Model.Axes[0].Zoom(min, max);
+            Model.Axes[1].Zoom(0, maxAnnotatedIntensity * YRangeMultiplier);
+        }
+        // Isolation Region or trimmed display region
+        else
+        {
+            Model.Title = $"Scan {scan.OneBasedScanNumber} (MS{scan.MsnOrder}) - Isolation Window {isolationRange!.Minimum:F2}-{isolationRange.Maximum:F2} m/z";
+
+            Model.Axes[0].Zoom(isolationRange.Minimum - 1, isolationRange.Maximum + 1);
+            Model.Axes[1].Zoom(0, maxAnnotatedIntensity * YRangeMultiplier);
+        }
+    }
+}
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawDataLoader.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawDataLoader.cs
new file mode 100644
index 000000000..3ae35638f
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawDataLoader.cs
@@ -0,0 +1,518 @@
+#nullable enable
+using EngineLayer;
+using Readers.SpectralLibrary;
+using Readers;
+using System;
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.Linq;
+using System.Threading;
+using System.Threading.Tasks;
+using System.Windows.Data;
+using System.Collections.Concurrent;
+using System.IO;
+using Readers.InternalResults;
+using MassSpectrometry;
+using Nett;
+using TaskLayer;
+
+namespace GuiFunctions.MetaDraw;
+
+public class MetaDrawDataLoader
+{
+    private readonly MetaDrawLogic _logic;
+    private CancellationTokenSource? _cancellationTokenSource;
+
+    public MetaDrawDataLoader(MetaDrawLogic logic)
+    {
+        _logic = logic;
+        BindingOperations.EnableCollectionSynchronization(LoadingProgressViewModel.Instance.Steps, _progressLock);
+    }
+
+    public async Task<List<string>> LoadAllAsync(
+        bool loadSpectra,
+        bool loadPsms,
+        bool loadLibraries,
+        ChimeraAnalysisTabViewModel? chimeraTabViewModel = null,
+        BioPolymerTabViewModel? bioPolymerTabViewModel = null,
+        DeconExplorationTabViewModel? deconExplorationTabViewModel = null)
+    {
+        // Cancel any previous run
+        _cancellationTokenSource?.Cancel();
+        _cancellationTokenSource = new CancellationTokenSource();
+        var token = _cancellationTokenSource.Token;
+        var allErrors = new List<string>();
+
+        // Prepare progress visualization
+        PrepareProgressVisualization(loadSpectra, loadPsms, loadLibraries, _logic);
+        if (chimeraTabViewModel is not null) 
+            chimeraTabViewModel.IsTabEnabled = false;
+        if (bioPolymerTabViewModel is not null) 
+            bioPolymerTabViewModel.IsTabEnabled = false;
+        if (deconExplorationTabViewModel is not null) 
+            deconExplorationTabViewModel.IsTabEnabled = false;
+
+        // Start core artifact loads (independent steps run concurrently)
+        var spectraTask = loadSpectra 
+            ? LoadSpectraAsync(token) 
+            : Task.FromResult(new List<string>());
+        var psmsTask = loadPsms 
+            ? LoadPsmsAsync(loadSpectra, token) 
+            : Task.FromResult(new List<string>());
+        var librariesTask = loadLibraries 
+            ? LoadLibrariesAsync(token) 
+            : Task.FromResult(new List<string>());
+        var proseAndTomlTask = _logic.SpectralMatchResultFilePaths.Any()
+            ? TryLoadProseAndSearchToml(bioPolymerTabViewModel, deconExplorationTabViewModel)
+            : Task.FromResult((false, false));
+
+        List<string>[] results;
+        try 
+        { 
+            results = await Task.WhenAll(spectraTask, psmsTask, librariesTask).ConfigureAwait(false); 
+        }
+        catch (OperationCanceledException) { return new() { "Loading was canceled." }; }
+
+        allErrors.AddRange(results.SelectMany(e => e));
+        if (token.IsCancellationRequested) return allErrors;
+
+        string outputDirectory = null!;
+        if (_logic.SpectralMatchResultFilePaths.Count > 0)
+        {
+            outputDirectory = Path.GetDirectoryName(_logic.SpectralMatchResultFilePaths.First()) ?? string.Empty;
+        }
+        else if (_logic.SpectraFilePaths.Count > 0)
+        {
+            outputDirectory = Path.GetDirectoryName(_logic.SpectraFilePaths.First()) ?? string.Empty;
+        }
+        else
+            outputDirectory = Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments);
+
+        await proseAndTomlTask;
+        // Tabs: run in background, post minimal changes to UI
+        if (bioPolymerTabViewModel is not null && _logic.AllSpectralMatches.Any())
+        {
+            Task.Run(() => ProcessBioPolymerTab(bioPolymerTabViewModel, outputDirectory, token), token);
+        }
+        if (deconExplorationTabViewModel is not null && _logic.MsDataFiles.Any())
+        {
+            Task.Run(() => ProcessDeconTab(deconExplorationTabViewModel, outputDirectory, token), token);
+        }
+        if (chimeraTabViewModel is not null && _logic.FilteredListOfPsms.Any() && _logic.MsDataFiles.Any())
+        {
+            Task.Run(() => ProcessChimeraTab(chimeraTabViewModel, outputDirectory, token), token);
+        }
+
+        return allErrors;
+    }
+
+    #region Core loaders (non-blocking)
+
+    public async Task<List<string>> LoadSpectraAsync(CancellationToken token)
+    {
+        var errors = new ConcurrentBag<string>();
+        var files = _logic.SpectraFilePaths.Where(path => File.Exists(path) || Directory.Exists(path)).ToArray();
+        var total = files.Length;
+        ReportProgress(StepSpectra, 0, total);
+
+        var maxDeg = Math.Max(2, Math.Min(Environment.ProcessorCount, 8));
+        var completed = 0;
+
+        await Task.Run(() =>
+        {
+            Parallel.ForEach(files,
+                new ParallelOptions { MaxDegreeOfParallelism = maxDeg, CancellationToken = token },
+                path =>
+                {
+                    token.ThrowIfCancellationRequested();
+
+                    var ext = GlobalVariables.GetFileExtension(path);
+                    var key = System.IO.Path.GetFileName(path.Replace(ext, string.Empty));
+
+                    var dataFile = MsDataFileReader.GetDataFile(path);
+                    try
+                    {
+                        if (dataFile is TimsTofFileReader tims)
+                        {
+                            tims.LoadAllStaticData(maxThreads: Math.Max(1, Environment.ProcessorCount - 1));
+                        }
+                        else
+                        {
+                            dataFile.InitiateDynamicConnection();
+                        }
+
+                        lock (_logic.ThreadLocker) // MsDataFiles is a Dictionary
+                        {
+                            if (!_logic.MsDataFiles.ContainsKey(key))
+                            {
+                                _logic.MsDataFiles.Add(key, dataFile);
+                            }
+                            else
+                            {
+                                dataFile.CloseDynamicConnection();
+                            }
+                        }
+                    }
+                    catch (Exception ex)
+                    {
+                        try { dataFile.CloseDynamicConnection(); } catch { /* best effort */ }
+                        errors.Add($"Error loading spectra file '{path}': {ex.Message}");
+                    }
+                    finally
+                    {
+                        var done = Interlocked.Increment(ref completed);
+                        ReportProgress(StepSpectra, done, total);
+                    }
+                });
+        }, token).ConfigureAwait(false);
+
+        return errors.ToList();
+    }
+
+    public async Task<List<string>> LoadPsmsAsync(bool requireMatchingSpectra, CancellationToken token)
+    {
+        var errors = new ConcurrentBag<string>();
+        var tsvs = _logic.SpectralMatchResultFilePaths;
+        var total = tsvs.Count;
+        ReportProgress(StepPsms, 0, total);
+
+        var spectraNames = new HashSet<string>(
+            _logic.SpectraFilePaths.Select(p =>
+            {
+                var ext = GlobalVariables.GetFileExtension(p);
+                return System.IO.Path.GetFileName(p.Replace(ext, string.Empty));
+            }),
+            StringComparer.OrdinalIgnoreCase);
+
+        var acceptedAll = new ConcurrentBag<SpectrumMatchFromTsv>();
+        var acceptedByFile = new ConcurrentDictionary<string, List<SpectrumMatchFromTsv>>();
+        var missingDueToNoSpectra = new ConcurrentBag<SpectrumMatchFromTsv>();
+        var maxDeg = Math.Max(2, Math.Min(Environment.ProcessorCount, 8));
+        var completed = 0;
+
+        await Task.Run(() =>
+        {
+            Parallel.ForEach(tsvs,
+                new ParallelOptions { MaxDegreeOfParallelism = maxDeg, CancellationToken = token },
+                rf =>
+                {
+                    token.ThrowIfCancellationRequested();
+                    try
+                    {
+                        var psms = SpectrumMatchTsvReader.ReadTsv(rf, out var warnings);
+                        foreach (var w in warnings)
+                        {
+                            errors.Add($"Warning parsing '{rf}': {w}");
+                        }
+
+                        foreach (var p in psms)
+                        {
+                            bool hasMatchingSpectra = spectraNames.Contains(p.FileNameWithoutExtension);
+                            if (!requireMatchingSpectra || hasMatchingSpectra)
+                            {
+                                acceptedAll.Add(p);
+                                acceptedByFile.AddOrUpdate(p.FileNameWithoutExtension,
+                                    _ => new List<SpectrumMatchFromTsv> { p },
+                                    (_, list) => { list.Add(p); return list; });
+                            }
+                            else
+                            {
+                                missingDueToNoSpectra.Add(p);
+                            }
+                        }
+                    }
+                    catch (Exception ex) { errors.Add($"Error reading PSM file:\n{ex}"); }
+                    finally
+                    {
+                        var done = Interlocked.Increment(ref completed);
+                        ReportProgress(StepPsms, done, total);
+                    }
+                });
+        }, token).ConfigureAwait(false);
+
+        // Merge once; FilteredListOfPsms & grouped dict are already collection-synchronized
+        lock (_logic.ThreadLocker)
+        {
+            _logic.AllSpectralMatches.AddRange(acceptedAll
+                .OrderByDescending(p => p is PsmFromTsv { BetaPeptideScore: not null } psm 
+                    ? p.Score + psm.BetaPeptideScore.Value
+                    : p.Score
+                )
+                .ThenByDescending(p => p.DeltaScore));
+            foreach (var kv in acceptedByFile)
+            {
+                var ordered = kv.Value
+                    .OrderByDescending(p => p is PsmFromTsv { BetaPeptideScore: not null } psm
+                        ? p.Score + psm.BetaPeptideScore.Value
+                        : p.Score
+                    )
+                    .ThenByDescending(p => p.DeltaScore);
+                if (_logic.SpectralMatchesGroupedByFile.TryGetValue(kv.Key, out var existing))
+                {
+                    foreach (var p in ordered) 
+                        existing.Add(p);
+                }
+                else
+                {
+                    _logic.SpectralMatchesGroupedByFile[kv.Key] = new(ordered);
+                }
+            }
+
+            _logic.FilterPsms(); 
+        }
+
+        // Missing spectra messages (after merge)
+        var missingMsgs = missingDueToNoSpectra
+            .GroupBy(p => p.FileNameWithoutExtension, StringComparer.OrdinalIgnoreCase)
+            .Select(g => $"{g.Count()} PSMs from {g.Key} were not loaded because this spectra file was not found");
+
+        foreach (var m in missingMsgs) 
+            errors.Add(m);
+        return errors.ToList();
+    }
+
+    public async Task<List<string>> LoadLibrariesAsync(CancellationToken token)
+    {
+        var errors = new List<string>();
+        var total = Math.Max(1, _logic.SpectralLibraryPaths.Count);
+        ReportProgress(StepLibraries, 0, total);
+
+        try
+        {
+            await Task.Run(() =>
+            {
+                token.ThrowIfCancellationRequested();
+                if (_logic.SpectralLibraryPaths.Count > 0)
+                {
+                    _logic.SpectralLibrary = new SpectralLibrary(_logic.SpectralLibraryPaths.ToList());
+                }
+            }, token).ConfigureAwait(false);
+        }
+        catch (OperationCanceledException) { throw; }
+        catch (Exception e)
+        {
+            _logic.SpectralLibrary = null;
+            errors.Add("Problem loading spectral library: " + e.Message);
+        }
+        finally
+        {
+            ReportProgress(StepLibraries, total, total);
+        }
+
+        return errors;
+    }
+
+    public async Task<(bool Database, bool SearchParams)> TryLoadProseAndSearchToml(BioPolymerTabViewModel? bpTabVm, DeconExplorationTabViewModel? deconTabVm)
+    {
+        bool loadedDb = false;
+        bool loadedSearchParams = false;
+
+        var searchDirectories = _logic.SpectralMatchResultFilePaths
+            .Select(Path.GetDirectoryName)
+            .Where(p => p != null)
+            .Select(p =>
+            {
+                // If directory name contains "Individual File Results", go up one parent
+                if (Path.GetFileName(p)?.Contains("Individual File Results", StringComparison.OrdinalIgnoreCase) ?? false)
+                {
+                    var parent = Directory.GetParent(p!);
+                    return parent?.FullName ?? p;
+                }
+                return p;
+            })
+            .Distinct()
+            .ToArray();
+
+        // Try to find search tomls to load decon parameters. 
+        try
+        {
+            HashSet<string?> distinctSearchTomls = new();
+            foreach (var searchDir in searchDirectories)
+            {
+                if (searchDir == null) 
+                    continue;
+
+                var parentDir = Directory.GetParent(searchDir)?.FullName ?? null;
+                var searchDirName = Path.GetFileName(searchDir);
+
+                if (parentDir == null) 
+                    continue;
+
+                // Attempt to locate search toml
+                var settingsDir = Directory.GetDirectories(parentDir).FirstOrDefault(p => p.Contains("Task Settings"));
+                if (settingsDir != null)
+                {
+                    distinctSearchTomls.Add(
+                        Directory.GetFiles(settingsDir, $"*{searchDirName}config.toml").FirstOrDefault());
+                }
+            }
+
+            List<DeconvolutionParameters> precursorParameters = new();
+            List<DeconvolutionParameters> productParameters = new();
+
+            foreach (var searchToml in distinctSearchTomls.Where(p => p != null))
+            {
+                var task = Toml.ReadFile<SearchTask>(searchToml, MetaMorpheusTask.tomlConfig);
+                precursorParameters.Add(task.CommonParameters.PrecursorDeconvolutionParameters);
+                productParameters.Add(task.CommonParameters.ProductDeconvolutionParameters);
+            }
+
+            // IF we find params, and have multiple, take the last. 
+            // Not the best way to do it, but without an equality comparison on decon params, it's hard to know if they are different or identical. 
+            if (precursorParameters.Any() && productParameters.Any())
+            {
+                var precursor = precursorParameters.Last();
+                var product = productParameters.Last();
+                MetaDrawSettingsViewModel.Instance.DeconHostViewModel = new(precursor, product);
+                loadedSearchParams = true;
+
+                if (deconTabVm != null) 
+                {
+                    deconTabVm.DeconHostViewModel = new(precursor, product);
+                }
+            }
+        }
+        catch (Exception) { loadedSearchParams = false; }
+
+        if (bpTabVm is null)
+            return (loadedDb, loadedSearchParams);
+
+        string[] acceptableDbTypes = new[] { ".fasta", ".fa", ".xml" };
+
+        // Try to find databases from the prose files. 
+        try
+        {
+            List<string> databases = new();
+            foreach (var searchDir in searchDirectories)
+            {
+                if (searchDir == null) 
+                    continue;
+                var proseFile = MetaMorpheusProseFile.LocateInDirectory(searchDir);
+                if (proseFile == null) 
+                    continue;
+                databases.AddRange(proseFile.DatabasePaths);
+            }
+
+            // Db tab only supports one database at a time currently, pick the one which occurs the most, then first in order
+            foreach (var dbGroup in databases
+                .Where(p => File.Exists(p) && acceptableDbTypes.Any(p.Contains))
+                            .GroupBy(db => db, StringComparer.OrdinalIgnoreCase)
+                            .OrderByDescending(g => g.Count())
+                            .ThenBy(g => databases.IndexOf(g.Key)))
+            {
+                bpTabVm.DatabasePath = dbGroup.Key;
+                loadedDb = true;
+                break;
+            }
+        }
+        catch (Exception) { loadedDb = false; }
+
+
+        return (loadedDb, loadedSearchParams);
+    }
+
+    #endregion
+
+    #region Tab Processing 
+
+    private void ProcessBioPolymerTab(BioPolymerTabViewModel tab, string outDir, CancellationToken token)
+    {
+        if (token.IsCancellationRequested) return;
+
+        // Load DB if present but not loaded
+        if (!tab.IsDatabaseLoaded && !string.IsNullOrEmpty(tab.DatabasePath))
+        {
+            tab.LoadDatabaseCommand.Execute(null);
+        }
+
+        if (tab.IsDatabaseLoaded)
+        {
+            tab.ProcessSpectralMatches(_logic.AllSpectralMatches, token);
+        }
+
+        tab.ExportDirectory = outDir;
+        tab.IsTabEnabled = true;
+    }
+
+    private void ProcessDeconTab(DeconExplorationTabViewModel tab, string outDir, CancellationToken token)
+    {
+        if (token.IsCancellationRequested) 
+            return;
+
+        tab.MsDataFiles.Clear();
+        foreach (var file in _logic.MsDataFiles.Values)
+        {
+            tab.MsDataFiles.Add(file);
+        }
+
+        tab.ExportDirectory = outDir;
+        tab.IsTabEnabled = true;
+    }
+
+    private void ProcessChimeraTab(ChimeraAnalysisTabViewModel tab, string outDir, CancellationToken token)
+    {
+        if (token.IsCancellationRequested) 
+            return;
+
+        tab.ProcessChimeraData(_logic.FilteredListOfPsms.ToList(), _logic.MsDataFiles, token);
+
+        tab.ExportDirectory = outDir;
+        tab.IsTabEnabled = true;
+    }
+
+    #endregion
+
+    #region UI Progress
+
+    private readonly object _progressLock = new();
+    private readonly Dictionary<string, LoadingStepViewModel> _steps = new(StringComparer.Ordinal);
+    private const string StepSpectra = "Loading Spectra Files";
+    private const string StepPsms = "Loading Search Results";
+    private const string StepLibraries = "Loading Spectral Libraries";
+
+    private void PrepareProgressVisualization(
+        bool loadSpectra, bool loadPsms, bool loadLibraries, MetaDrawLogic logic)
+    {
+        var vm = LoadingProgressViewModel.Instance;
+        lock (_progressLock)
+        {
+            vm.Steps.Clear();
+            _steps.Clear();
+
+            if (loadSpectra && logic.SpectraFilePaths.Count > 0)
+                AddStep(StepSpectra, logic.SpectraFilePaths.Count);
+
+            if (loadPsms && logic.SpectralMatchResultFilePaths.Count > 0)
+                AddStep(StepPsms, logic.SpectralMatchResultFilePaths.Count);
+
+            if (loadLibraries && logic.SpectralLibraryPaths.Count > 0)
+                AddStep(StepLibraries, Math.Max(1, logic.SpectralLibraryPaths.Count));
+
+            vm.IsVisible = vm.Steps.Any();
+        }
+    }
+
+    private void AddStep(string name, int total)
+    {
+        var step = new LoadingStepViewModel { StepName = name, Total = total, Current = 0 };
+        LoadingProgressViewModel.Instance.Steps.Add(step);
+        _steps[name] = step;
+    }
+
+    private void ReportProgress(string stepName, int current, int total)
+    {
+        lock (_progressLock)
+        {
+            if (_steps.TryGetValue(stepName, out var s))
+            {
+                s.Total = total;
+                s.Current = current;
+            }
+            LoadingProgressViewModel.Instance.IsVisible =
+                LoadingProgressViewModel.Instance.Steps.Any(st => st.Current < st.Total);
+        }
+    }
+
+    #endregion
+}
+
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
index 73c2c2a64..d0a1d71a0 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
@@ -1,5 +1,4 @@
 global using PsmFromTsv = Readers.PsmFromTsv; // Temporary until a follow-up PR changes these to SpectrumMatchFromTsv
-using EngineLayer;
 using iText.IO.Image;
 using iText.Kernel.Pdf;
 using MassSpectrometry;
@@ -22,9 +21,9 @@
 using System.Threading;
 using Omics.Fragmentation;
 using Omics.SpectrumMatch;
-using System.Reflection;
 using System.Runtime.CompilerServices;
 using Readers.SpectralLibrary;
+using GuiFunctions.MetaDraw;
 
 [assembly: InternalsVisibleTo("Test")]
 namespace GuiFunctions
@@ -43,11 +42,11 @@ public class MetaDrawLogic
         public object ThreadLocker;
         public ICollectionView PeptideSpectralMatchesView;
 
-        private List<SpectrumMatchFromTsv> AllSpectralMatches; // all loaded PSMs
+        public List<SpectrumMatchFromTsv> AllSpectralMatches; // all loaded PSMs
         public Dictionary<string, MsDataFile> MsDataFiles { get; } // key is file name without extension
         private List<SpectrumMatchPlot> CurrentlyDisplayedPlots;
         private Regex illegalInFileName = new Regex(@"[\\/:*?""<>|]");
-        private SpectralLibrary SpectralLibrary;
+        public SpectralLibrary SpectralLibrary { get; set; }
 
         public MetaDrawLogic()
         {
@@ -61,41 +60,16 @@ public MetaDrawLogic()
             PeptideSpectralMatchesView = CollectionViewSource.GetDefaultView(FilteredListOfPsms);
             ThreadLocker = new object();
             CurrentlyDisplayedPlots = new List<SpectrumMatchPlot>();
-        }
-
-        public List<string> LoadFiles(bool loadSpectra, bool loadPsms)
-        {
-            List<string> errors = new List<string>();
-
-            lock (ThreadLocker)
-            {
-                FilteredListOfPsms.Clear();
-                SpectralMatchesGroupedByFile.Clear();
-                AllSpectralMatches.Clear();
-                MsDataFiles.Clear();
-            }
-
-            // load MS data files
-            if (loadSpectra)
-            {
-                LoadSpectraFiles(out var errors1);
-                errors.AddRange(errors1);
-            }
 
-            // load PSMs
-            if (loadPsms)
-            {
-                LoadPsms(out var errors2, loadSpectra);
-                errors.AddRange(errors2);
-            }
-
-            // load spectral libraries
-            LoadSpectralLibraries(out var errors3);
-            errors.AddRange(errors3);
-
-            return errors;
+            // Enable cross-thread synchronization 
+            BindingOperations.EnableCollectionSynchronization(SpectralMatchResultFilePaths, ThreadLocker);
+            BindingOperations.EnableCollectionSynchronization(SpectraFilePaths, ThreadLocker);
+            BindingOperations.EnableCollectionSynchronization(FilteredListOfPsms, ThreadLocker);
+            BindingOperations.EnableCollectionSynchronization(SpectralMatchesGroupedByFile, ThreadLocker);
         }
 
+        #region Plot Generation 
+
         public void DisplaySpectrumMatch(PlotView plotView, SpectrumMatchFromTsv sm, ParentChildScanPlotsView parentChildScanPlotsView, out List<string> errors)
         {
             errors = null;
@@ -112,7 +86,6 @@ public void DisplaySpectrumMatch(PlotView plotView, SpectrumMatchFromTsv sm, Par
                 return;
             }
 
-            spectraFile.InitiateDynamicConnection();
             MsDataScan scan = spectraFile.GetOneBasedScanFromDynamicConnection(sm.Ms2ScanNumber);
 
             LibrarySpectrum librarySpectrum = null;
@@ -225,7 +198,6 @@ public void DisplaySpectrumMatch(PlotView plotView, SpectrumMatchFromTsv sm, Par
 
                     CurrentlyDisplayedPlots.Add(childPlot);
                 }
-                spectraFile.CloseDynamicConnection();
             }
         }
 
@@ -480,6 +452,17 @@ public static void DrawLine(Canvas cav, Point start, Point end, Color clr)
             Canvas.SetZIndex(line, 1); //on top of any other things in canvas
         }
 
+        #endregion
+
+        public MsDataScan GetMs2ScanFromPsm(SpectrumMatchFromTsv spectralMatch)
+        {
+            return !MsDataFiles.TryGetValue(spectralMatch.FileNameWithoutExtension, out MsDataFile spectraFile) 
+                ? null 
+                : spectraFile.GetOneBasedScanFromDynamicConnection(spectralMatch.Ms2ScanNumber);
+        }
+
+        #region Plot Export
+
         public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<SpectrumMatchFromTsv> spectrumMatches,
             ParentChildScanPlotsView parentChildScanPlotsView, string directory, out List<string> errors,
             Canvas legendCanvas = null, Vector ptmLegendLocationVector = new(), FragmentationReanalysisViewModel? reFragment = null)
@@ -490,7 +473,7 @@ public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<Spectrum
             {
                 Directory.CreateDirectory(directory);
             }
-            
+
             foreach (var psm in spectrumMatches)
             {
                 // get the scan
@@ -515,11 +498,10 @@ public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<Spectrum
                     DisplaySequences(stationaryCanvas, null, null, psm);
                     DisplaySpectrumMatch(plotView, psm, parentChildScanPlotsView, out errors);
                 }
-                
 
                 if (errors != null)
                 {
-                    errors.AddRange(errors); 
+                    errors.AddRange(errors);
                 }
 
                 string sequence = psm.IsPeptide()
@@ -535,12 +517,12 @@ public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<Spectrum
 
                 foreach (var plot in CurrentlyDisplayedPlots)
                 {
-                    string filePath = System.IO.Path.Combine(directory, plot.Scan.OneBasedScanNumber + "_" + sequence + "." + MetaDrawSettings.ExportType);
+                    string filePath = System.IO.Path.Combine(directory, plot.Scan.OneBasedScanNumber + "_" + sequence + "." + MetaDrawSettings.ExportType.ToLower());
 
                     int i = 2;
                     while (File.Exists(filePath))
                     {
-                        filePath = System.IO.Path.Combine(directory, plot.Scan.OneBasedScanNumber + "_" + sequence + "_" + i + "." + MetaDrawSettings.ExportType);
+                        filePath = System.IO.Path.Combine(directory, plot.Scan.OneBasedScanNumber + "_" + sequence + "_" + i + "." + MetaDrawSettings.ExportType.ToLower());
                         i++;
                     }
 
@@ -588,13 +570,6 @@ public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<Spectrum
             }
         }
 
-        public MsDataScan GetMs2ScanFromPsm(SpectrumMatchFromTsv spectralMatch)
-        {
-            return !MsDataFiles.TryGetValue(spectralMatch.FileNameWithoutExtension, out MsDataFile spectraFile) 
-                ? null 
-                : spectraFile.GetOneBasedScanFromDynamicConnection(spectralMatch.Ms2ScanNumber);
-        }
-
         /// <summary>
         /// Exports the sequence coverage view to an image file
         /// </summary>
@@ -616,7 +591,7 @@ public void ExportSequenceCoverage(Canvas textCanvas, Canvas mapCanvas, string d
             {
                 sequence = sequence.Substring(0, 30);
             }
-            string path = System.IO.Path.Combine(directory, sm.Ms2ScanNumber + "_" + sequence + "_SequenceCoverage." + MetaDrawSettings.ExportType);
+            string path = System.IO.Path.Combine(directory, sm.Ms2ScanNumber + "_" + sequence + "_SequenceCoverage." + MetaDrawSettings.ExportType.ToLower());
 
             // convert to format for export
             System.Drawing.Bitmap textBitmap = ConvertCanvasToBitmap(textCanvas, directory);
@@ -652,7 +627,7 @@ public void ExportAnnotatedSequence(Canvas sequenceAnnotaitonCanvas, System.Wind
             {
                 sequence = sequence.Substring(0, 30);
             }
-            string path = System.IO.Path.Combine(directory, psm.Ms2ScanNumber + "_" + sequence + "_SequenceAnnotation." + MetaDrawSettings.ExportType);
+            string path = System.IO.Path.Combine(directory, psm.Ms2ScanNumber + "_" + sequence + "_SequenceAnnotation." + MetaDrawSettings.ExportType.ToLower());
             int rows = (int)Math.Ceiling((double)psm.BaseSeq.Length / (MetaDrawSettings.SequenceAnnotaitonResiduesPerSegment * MetaDrawSettings.SequenceAnnotationSegmentPerRow)); ;
 
             // convert to format for export
@@ -737,6 +712,8 @@ public static System.Drawing.Bitmap CombineBitmap(List<System.Drawing.Bitmap> im
             }
         }
 
+        #endregion
+
         public void FilterPsms()
         {
             lock (ThreadLocker)
@@ -767,6 +744,21 @@ public void FilterPsmsByString(string searchString)
             }
         }
 
+        #region Resource Management
+
+        public List<string> LoadFiles(bool loadSpectra, bool loadPsms)
+        {
+            lock (ThreadLocker)
+            {
+                FilteredListOfPsms.Clear();
+                SpectralMatchesGroupedByFile.Clear();
+                AllSpectralMatches.Clear();
+                MsDataFiles.Clear();
+            }
+
+            return new MetaDrawDataLoader(this).LoadAllAsync(loadSpectra, loadPsms, true).Result;
+        }
+
         public void CleanUpResources()
         {
             lock (ThreadLocker)
@@ -819,6 +811,8 @@ public void CleanUpCurrentlyDisplayedPlots()
                 CurrentlyDisplayedPlots.Clear();
         }
 
+        #endregion
+
         #region Private Helpers
 
         /// <summary>
@@ -951,104 +945,6 @@ internal static void ExportBitmap(System.Drawing.Bitmap bitmap, string path)
                     break;
             }
         }
-
-        private void LoadPsms(out List<string> errors, bool haveLoadedSpectra)
-        {
-            errors = new List<string>();
-
-            HashSet<string> fileNamesWithoutExtension = new HashSet<string>(
-                SpectraFilePaths.Select(p => System.IO.Path.GetFileName(p.Replace(GlobalVariables.GetFileExtension(p), string.Empty))));
-            List<SpectrumMatchFromTsv> psmsThatDontHaveMatchingSpectraFile = new List<SpectrumMatchFromTsv>();
-
-            try
-            {
-                foreach (var resultsFile in SpectralMatchResultFilePaths)
-                {
-                    lock (ThreadLocker)
-                    {
-                        var psms = SpectrumMatchTsvReader.ReadTsv(resultsFile, out List<string> warnings);
-                        foreach (SpectrumMatchFromTsv psm in psms)
-                        {
-                            if (fileNamesWithoutExtension.Contains(psm.FileNameWithoutExtension) || !haveLoadedSpectra)
-                            {
-                                AllSpectralMatches.Add(psm);
-                            }
-                            else
-                            {
-                                psmsThatDontHaveMatchingSpectraFile.Add(psm);
-                            }
-
-                            if (SpectralMatchesGroupedByFile.TryGetValue(psm.FileNameWithoutExtension, out var psmsForThisFile))
-                            {
-                                psmsForThisFile.Add(psm);
-                            }
-                            else
-                            {
-                                SpectralMatchesGroupedByFile.Add(psm.FileNameWithoutExtension, new ObservableCollection<SpectrumMatchFromTsv> { psm });
-                            }
-                        }
-                    }
-                }
-            }
-            catch (Exception e)
-            {
-                errors.Add("Error reading PSM file:\n" + e.Message);
-            }
-
-            if (psmsThatDontHaveMatchingSpectraFile.Any())
-            {
-                foreach (var file in psmsThatDontHaveMatchingSpectraFile.GroupBy(p => p.FileNameWithoutExtension))
-                {
-                    errors.Add(file.Count() + " PSMs from " + file.Key + " were not loaded because this spectra file was not found");
-                }
-            }
-
-            FilterPsms();
-        }
-
-        private void LoadSpectraFiles(out List<string> errors)
-        {
-            errors = new List<string>();
-
-            foreach (var filepath in SpectraFilePaths)
-            {
-                lock (ThreadLocker)
-                {
-                    var fileNameWithoutExtension = System.IO.Path.GetFileName(filepath.Replace(GlobalVariables.GetFileExtension(filepath), string.Empty));
-                    var spectraFile = MsDataFileReader.GetDataFile(filepath);
-                    if (spectraFile is TimsTofFileReader timsTofDataFile)
-                    {
-                        timsTofDataFile.LoadAllStaticData(maxThreads: Environment.ProcessorCount - 1); // timsTof files need to load all static data before they can be used, as dynamic access is not available for them
-                    }
-                    else
-                    {
-                        spectraFile.InitiateDynamicConnection();
-                    }
-
-                    if (!MsDataFiles.TryAdd(fileNameWithoutExtension, spectraFile))
-                    {
-                        spectraFile.CloseDynamicConnection();
-                        // print warning? but probably unnecessary. this means the data file was loaded twice. 
-                        // which is an error but not an important one because the data is loaded
-                    }
-                }
-            }
-        }
-
-        private void LoadSpectralLibraries(out List<string> errors)
-        {
-            errors = new List<string>();
-
-            try
-            {
-                SpectralLibrary = new SpectralLibrary(SpectralLibraryPaths.ToList());
-            }
-            catch (Exception e)
-            {
-                SpectralLibrary = null;
-                errors.Add("Problem loading spectral library: " + e.Message);
-            }
-        }
     }
 
     #endregion
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs
index 5ef865824..c6f408cc6 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs
@@ -9,6 +9,7 @@
 using System.Windows.Media;
 using Readers;
 using GuiFunctions.MetaDraw;
+using OxyPlot.Wpf;
 
 namespace GuiFunctions
 {
@@ -76,7 +77,11 @@ public static class MetaDrawSettings
         public static string AmbiguityFilter { get; set; } = "No Filter";
         public static LocalizationLevel LocalizationLevelStart { get; set; } = LocalizationLevel.Level1;
         public static LocalizationLevel LocalizationLevelEnd { get; set; } = LocalizationLevel.Level3;
-        public static string ExportType { get; set; } = "Pdf"; 
+        public static string ExportType { get; set; } = "Pdf";
+
+        // biopolymer coverage settings
+        public static int BioPolymerCoverageFontSize { get; set; } = 16;
+        public static Dictionary<BioPolymerCoverageType, SolidColorBrush> BioPolymerCoverageColors { get; set; }
 
         #endregion
 
@@ -160,6 +165,7 @@ private static void InitializeDictionaries()
             ModificationTypeToColor = GlobalVariables.AllModsKnownDictionary.Values.ToDictionary(p => p.IdWithMotif, p => OxyColors.Orange);
             SpectrumDescription = SpectrumDescriptors.ToDictionary(p => p, p => true);
             CoverageTypeToColor = CoverageTypes.ToDictionary(p => p, p => OxyColors.Blue);
+            BioPolymerCoverageColors = Enum.GetValues<BioPolymerCoverageType>().ToDictionary(p => p, _ => Brushes.LightGray);
 
             // If no default settings are saved, load in defaults
             string settingsPath = Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"MetaDrawSettingsDefault.xml");
@@ -297,6 +303,7 @@ private static void SetDefaultColors()
             SetDefaultModificationColors();
             SetDefaultSpectrumDescriptors();
             SetDefaultDataVisualizationColors();
+            SetDefaultBioPolymerCoverageColors();
 
             UnannotatedPeakColor = OxyColors.LightGray;
             InternalIonColor = OxyColors.Purple;
@@ -419,6 +426,19 @@ private static void SetDefaultDataVisualizationColors()
             };
         }
 
+        private static void SetDefaultBioPolymerCoverageColors()
+        {
+            BioPolymerCoverageColors = new()
+            {
+                { BioPolymerCoverageType.Unique, Brushes.LightGreen },
+                { BioPolymerCoverageType.UniqueMissedCleavage, Brushes.YellowGreen },
+                { BioPolymerCoverageType.TandemRepeat, Brushes.LightBlue },
+                { BioPolymerCoverageType.TandemRepeatMissedCleavage, Brushes.SkyBlue },
+                { BioPolymerCoverageType.Shared, Brushes.Orange },
+                { BioPolymerCoverageType.SharedMissedCleavage, Brushes.OrangeRed }
+            };
+        }
+
         /// <summary>
         /// Lines to be written on the spectrum in the upper right hand corner
         /// </summary>
@@ -495,6 +515,8 @@ public static MetaDrawSettingsSnapshot MakeSnapShot()
                 NormalizeHistogramToFile = NormalizeHistogramToFile,
                 DisplayFilteredOnly = DisplayFilteredOnly,
                 DataVisualizationColorOrder = DataVisualizationColorOrder?.Select(c => c.GetColorName()).ToList(),
+                BioPolymerCoverageFontSize = BioPolymerCoverageFontSize,
+                BioPolymerCoverageColors = BioPolymerCoverageColors.Select(p => $"{p.Key},{p.Value.ToOxyColor().GetColorName()}").ToList()
             };
         }
 
@@ -537,6 +559,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
             ChimeraLegendMaxWidth = settings.ChimeraLegendMaxWidth;
             NormalizeHistogramToFile = settings.NormalizeHistogramToFile;
             DisplayFilteredOnly = settings.DisplayFilteredOnly;
+            BioPolymerCoverageFontSize = settings.BioPolymerCoverageFontSize;
 
             try // Product Type Colors
             {
@@ -741,6 +764,30 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
                 SetDefaultDataVisualizationColors();
                 flaggedErrorOnRead = true;
             }
+
+            // BioPolymer Coverage visualization colors
+            try
+            {
+                if (settings.BioPolymerCoverageColors is { Count: > 0 })
+                {
+                    foreach (var savedProductType in settings.BioPolymerCoverageColors)
+                    {
+                        var key = savedProductType.Split(',')[0];
+                        var color = savedProductType.Split(',')[1];
+                        var enumVal = Enum.Parse<BioPolymerCoverageType>(key);
+                        BioPolymerCoverageColors[enumVal] = DrawnSequence.ParseColorBrushFromName(color);
+                    }
+                }
+                else
+                {
+                    throw new Exception();
+                }
+            }
+            catch (Exception)
+            {
+                SetDefaultBioPolymerCoverageColors();
+                flaggedErrorOnRead = true;
+            }
         }
 
         #endregion
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs
index 98cf6cccb..977903348 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs
@@ -56,5 +56,10 @@ public class MetaDrawSettingsSnapshot
         public LocalizationLevel LocalizationLevelStart { get; set; } = LocalizationLevel.Level1;
         public LocalizationLevel LocalizationLevelEnd { get; set; } = LocalizationLevel.Level3;
         public string ExportType { get; set; }
+
+        // BioPolymer coverage settings
+
+        public int BioPolymerCoverageFontSize { get; set; } = 16;
+        public List<string> BioPolymerCoverageColors { get; set; }
     }
 }
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/ChimeraSpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/ChimeraSpectrumMatchPlot.cs
index 8ca8502a6..a288c9e45 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/ChimeraSpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/ChimeraSpectrumMatchPlot.cs
@@ -28,13 +28,13 @@ public ChimeraSpectrumMatchPlot(PlotView plotView, ChimeraGroupViewModel chimera
                     matchedIons.Add(group[i].Item1);
             MatchedFragmentIons = matchedIons;
 
+            ZoomAxes();
             AnnotateMatchedIons(chimeraGroupVm);
             if (Math.Abs(mzMax - double.MaxValue) > 0.001)
             {
                 Model.Axes[0].Maximum = mzMax;
             }
 
-            ZoomAxes();
             RefreshChart();
         }
 
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
new file mode 100644
index 000000000..a46b4d69f
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
@@ -0,0 +1,231 @@
+using System;
+using System.Drawing;
+using System.IO;
+using System.Linq;
+using iText.IO.Image;
+using iText.Kernel.Pdf;
+using iText.Layout;
+using MassSpectrometry;
+using MzLibUtil;
+using OxyPlot;
+using OxyPlot.Axes;
+using OxyPlot.Wpf;
+using LinearAxis = OxyPlot.Axes.LinearAxis;
+using LineSeries = OxyPlot.Series.LineSeries;
+using Plot = mzPlot.Plot;
+using TextAnnotation = OxyPlot.Annotations.TextAnnotation;
+
+namespace GuiFunctions;
+
+public class MassSpectrumPlot : Plot
+{
+    private const int MultiLineAnnotationPixelSpacing = 18;
+    public PlotView PlotView { get; protected set; }
+    public MsDataScan Scan { get; private set; }
+    public MassSpectrumPlot(PlotView plotView, MsDataScan scan) : base(plotView)
+    {
+        PlotView = plotView;
+        Model.Title = string.Empty;
+        Model.Subtitle = string.Empty;
+        Scan = scan;
+        DrawSpectrum();
+        RefreshChart();
+    }
+
+    /// <summary>
+    /// Adds the spectrum from the MSDataScan to the Model
+    /// </summary>
+    protected void DrawSpectrum()
+    {
+        var yArray = Scan.MassSpectrum.YArray;
+        var xArray = Scan.MassSpectrum.XArray;
+        double yMax = 0;
+        for (int i = 0; i < yArray.Length; i++)
+        {
+            if (yArray[i] > yMax) yMax = yArray[i];
+        }
+        // set up axes
+        Model.Axes.Add(new LinearAxis
+        {
+            Position = AxisPosition.Bottom,
+            Title = "m/z",
+            Minimum = Scan.ScanWindowRange.Minimum,
+            Maximum = Scan.ScanWindowRange.Maximum,
+            AbsoluteMinimum = Math.Max(0, Scan.ScanWindowRange.Minimum - 100),
+            AbsoluteMaximum = Scan.ScanWindowRange.Maximum + 100,
+            MajorTickSize = 2,
+            TitleFontWeight = FontWeights.Bold,
+            TitleFontSize = MetaDrawSettings.AxisTitleTextSize,
+            FontSize = MetaDrawSettings.AxisLabelTextSize,
+        });
+
+        Model.Axes.Add(new LinearAxis
+        {
+            Position = AxisPosition.Left,
+            Title = "Intensity",
+            Minimum = 0,
+            Maximum = yMax,
+            AbsoluteMinimum = 0,
+            AbsoluteMaximum = yMax * 2,
+            StringFormat = "0e-0",
+            MajorTickSize = 2,
+            TitleFontWeight = FontWeights.Bold,
+            TitleFontSize = MetaDrawSettings.AxisTitleTextSize,
+            FontSize = MetaDrawSettings.AxisLabelTextSize,
+            AxisTitleDistance = 10,
+            ExtraGridlines = new double[] { 0 },
+            ExtraGridlineColor = OxyColors.Black,
+            ExtraGridlineThickness = 1
+        });
+
+        // Batch peaks into a single LineSeries for unannotated peaks
+        var unannotatedSeries = new LineSeries
+        {
+            Color = MetaDrawSettings.UnannotatedPeakColor,
+            StrokeThickness = MetaDrawSettings.StrokeThicknessUnannotated,
+            LineStyle = LineStyle.Solid
+        };
+
+        for (int i = 0; i < xArray.Length; i++)
+        {
+            double mz = xArray[i];
+            double intensity = yArray[i];
+            // Add as vertical line (two points per peak)
+            unannotatedSeries.Points.Add(new DataPoint(mz - 0.0001, 0));
+            unannotatedSeries.Points.Add(new DataPoint(mz, intensity));
+            unannotatedSeries.Points.Add(new DataPoint(mz + 0.0001, 0));
+        }
+        Model.Series.Add(unannotatedSeries);
+    }
+
+    /// <summary>
+    /// Draws a peak on the spectrum
+    /// </summary>
+    /// <param name="mz">x value of peak to draw</param>
+    /// <param name="intensity">y max of peak to draw</param>
+    /// <param name="strokeWidth"></param>
+    /// <param name="color">Color to draw peak</param>
+    /// <param name="annotation">text to display above the peak</param>
+    protected void DrawPeak(double mz, double intensity, double strokeWidth, OxyColor color,
+        TextAnnotation annotation)
+    {
+        // peak line
+        var line = new LineSeries
+        {
+            Color = color,
+            StrokeThickness = strokeWidth
+        };
+        line.Points.Add(new DataPoint(mz, 0));
+        line.Points.Add(new DataPoint(mz, intensity));
+
+        // Miso is a tag used in chimeric ms1 plotting to indicate that we should not annotate this peak with a label. 
+        if (annotation != null && !annotation.Text.Contains("Miso"))
+        {
+            var x = annotation.TextPosition.X;
+            var y = annotation.TextPosition.Y + 20;
+            var splits = annotation.Text.Split('\n');
+
+            // Calculate y step for annotation lines based on PlotView's actual height
+            var yAxis = Model.Axes.FirstOrDefault(a => a.Position == AxisPosition.Left);
+            double yRange = yAxis != null ? Math.Abs(yAxis.ActualMaximum - yAxis.ActualMinimum) : 1.0;
+            double plotHeight = PlotView?.ActualHeight > 0 ? PlotView.ActualHeight : 370.0; // fallback to default height
+            double yStep = yRange * (MultiLineAnnotationPixelSpacing / plotHeight); // Convert pixel spacing to y-axis units
+
+            for (int j = splits.Length - 1; j >= 0; j--)
+            {
+                var split = splits[j];
+                var annotationLine = new TextAnnotation
+                {
+                    Font = annotation.Font,
+                    FontSize = annotation.FontSize,
+                    FontWeight = annotation.FontWeight,
+                    TextColor = annotation.TextColor,
+                    StrokeThickness = annotation.StrokeThickness,
+                    Text = split,
+                    TextPosition = new DataPoint(x, y),
+                    TextVerticalAlignment = annotation.TextVerticalAlignment,
+                    TextHorizontalAlignment = HorizontalAlignment.Center
+                };
+                Model.Annotations.Add(annotationLine);
+                y += yStep;
+            }
+        }
+
+        Model.Series.Add(line);
+    }
+
+    protected void AnnotateIsolationWindow(DoubleRange isolationRange)
+    {
+        var yMax = Model.Axes[1].AbsoluteMaximum;
+        var points = new DataPoint[]
+        {
+            new(isolationRange.Minimum, yMax),
+            new(isolationRange.Minimum, 0),
+            new(isolationRange.Maximum, 0),
+            new(isolationRange.Maximum, yMax),
+        };
+        var lineSeries = new LineSeries
+        {
+            LineStyle = LineStyle.Dash,
+            Color = OxyColors.Red
+        };
+        lineSeries.Points.AddRange(points);
+        Model.Series.Add(lineSeries);
+    }
+
+    /// <summary>
+    /// Exports plot from a combined bitmap created in the children classes
+    /// </summary>
+    /// <param name="path"></param>
+    /// <param name="combinedBitmaps"></param>
+    /// <param name="width"></param>
+    /// <param name="height"></param>
+    public static void ExportPlot(string path, Bitmap combinedBitmaps, double width = 700, double height = 370)
+    {
+        width = width > 0 ? width : 700;
+        height = height > 0 ? height : 300;
+        switch (MetaDrawSettings.ExportType)
+        {
+            case "Pdf":
+                string tempCombinedPath =
+                    System.IO.Path.Combine(System.IO.Path.GetDirectoryName(path), "tempCombined.png");
+                combinedBitmaps.Save(tempCombinedPath, System.Drawing.Imaging.ImageFormat.Png);
+
+                PdfDocument pdfDoc = new(new PdfWriter(path));
+                Document document = new(pdfDoc,
+                    new iText.Kernel.Geom.PageSize((float)width - 30, (float)height - 30));
+
+                ImageData sequenceAndLegendImageData = ImageDataFactory.Create(tempCombinedPath);
+                iText.Layout.Element.Image sequenceAndPtmLegendImage = new(sequenceAndLegendImageData);
+                sequenceAndPtmLegendImage.SetMarginLeft(-30);
+                sequenceAndPtmLegendImage.SetMarginTop(-30);
+                sequenceAndPtmLegendImage.ScaleToFit((float)width, (float)height);
+                document.Add(sequenceAndPtmLegendImage);
+
+                pdfDoc.Close();
+                document.Close();
+                File.Delete(tempCombinedPath);
+                break;
+
+            case "Png":
+                combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Png);
+                break;
+
+            case "Jpeg":
+                combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Jpeg);
+                break;
+
+            case "Tiff":
+                combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Tiff);
+                break;
+
+            case "Wmf":
+                combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Wmf);
+                break;
+
+            case "Bmp":
+                combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Bmp);
+                break;
+        }
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index dff4f632d..81b8ca4df 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -1,36 +1,28 @@
 using System;
 using System.Collections.Generic;
-using System.Drawing;
 using System.Globalization;
-using System.IO;
 using System.Linq;
 using System.Text;
 using Chemistry;
-using iText.IO.Image;
-using iText.Kernel.Pdf;
-using iText.Layout;
 using MassSpectrometry;
-using mzPlot;
 using Omics.Fragmentation;
 using Omics.SpectrumMatch;
 using OxyPlot;
-using OxyPlot.Annotations;
-using OxyPlot.Axes;
-using OxyPlot.Series;
+using OxyPlot.Wpf;
 using Readers;
+using Annotation = OxyPlot.Annotations.Annotation;
 using FontWeights = OxyPlot.FontWeights;
 using HorizontalAlignment = OxyPlot.HorizontalAlignment;
+using TextAnnotation = OxyPlot.Annotations.TextAnnotation;
 using VerticalAlignment = OxyPlot.VerticalAlignment;
 
 namespace GuiFunctions
 {
-    public class SpectrumMatchPlot : Plot
+    public class SpectrumMatchPlot : MassSpectrumPlot
     {
         public static int MaxCharactersPerDescriptionLine = 32;
         public List<MatchedFragmentIon> MatchedFragmentIons { get; protected set; }
-        public MsDataScan Scan { get; protected set; }
         public SpectrumMatchFromTsv SpectrumMatch { get; set; }
-        public OxyPlot.Wpf.PlotView PlotView { get; protected set; }
 
         /// <summary>
         /// Base Spectrum match constructor
@@ -40,15 +32,12 @@ public class SpectrumMatchPlot : Plot
         /// <param name="sm">sm to plot</param>
         /// <param name="scan">spectrum to plot</param>
         /// <param name="matchedIons">glyco ONLY child matched ions</param>
-        public SpectrumMatchPlot(OxyPlot.Wpf.PlotView plotView, SpectrumMatchFromTsv sm,
-            MsDataScan scan, List<MatchedFragmentIon> matchedIons = null) : base(plotView)
+        public SpectrumMatchPlot(PlotView plotView, SpectrumMatchFromTsv sm,
+            MsDataScan scan, List<MatchedFragmentIon> matchedIons = null) : base(plotView, scan)
         {
-            PlotView = plotView;
             Model.Title = string.Empty;
             Model.Subtitle = string.Empty;
-            Scan = scan;
 
-            DrawSpectrum();
             if (matchedIons is null && sm is not null)
             {
                 SpectrumMatch = sm;
@@ -68,131 +57,6 @@ public SpectrumMatchPlot(OxyPlot.Wpf.PlotView plotView, SpectrumMatchFromTsv sm,
             RefreshChart();
         }
 
-        /// <summary>
-        /// Adds the spectrum from the MSDataScan to the Model
-        /// </summary>
-        protected void DrawSpectrum()
-        {
-            var yArray = Scan.MassSpectrum.YArray;
-            var xArray = Scan.MassSpectrum.XArray;
-            double yMax = 0;
-            for (int i = 0; i < yArray.Length; i++)
-            {
-                if (yArray[i] > yMax) yMax = yArray[i];
-            }
-            // set up axes
-            Model.Axes.Add(new LinearAxis
-            {
-                Position = AxisPosition.Bottom,
-                Title = "m/z",
-                Minimum = Scan.ScanWindowRange.Minimum,
-                Maximum = Scan.ScanWindowRange.Maximum,
-                AbsoluteMinimum = Math.Max(0, Scan.ScanWindowRange.Minimum - 100),
-                AbsoluteMaximum = Scan.ScanWindowRange.Maximum + 100,
-                MajorStep = 200,
-                MinorStep = 200,
-                MajorTickSize = 2,
-                TitleFontWeight = FontWeights.Bold,
-                TitleFontSize = MetaDrawSettings.AxisTitleTextSize,
-                FontSize = MetaDrawSettings.AxisLabelTextSize,
-            });
-
-            Model.Axes.Add(new LinearAxis
-            {
-                Position = AxisPosition.Left,
-                Title = "Intensity",
-                Minimum = 0,
-                Maximum = yMax,
-                AbsoluteMinimum = 0,
-                AbsoluteMaximum = yMax * 2,
-                MajorStep = yMax / 10,
-                MinorStep = yMax / 50,
-                StringFormat = "0e-0",
-                MajorTickSize = 2,
-                TitleFontWeight = FontWeights.Bold,
-                TitleFontSize = MetaDrawSettings.AxisTitleTextSize,
-                FontSize = MetaDrawSettings.AxisLabelTextSize,
-                AxisTitleDistance = 10,
-                ExtraGridlines = new double[] { 0 },
-                ExtraGridlineColor = OxyColors.Black,
-                ExtraGridlineThickness = 1
-            });
-
-            // Batch peaks into a single LineSeries for unannotated peaks
-            var unannotatedSeries = new LineSeries
-            {
-                Color = MetaDrawSettings.UnannotatedPeakColor,
-                StrokeThickness = MetaDrawSettings.StrokeThicknessUnannotated,
-                LineStyle = LineStyle.Solid
-            };
-
-            for (int i = 0; i < xArray.Length; i++)
-            {
-                double mz = xArray[i];
-                double intensity = yArray[i];
-                // Add as vertical line (two points per peak)
-                unannotatedSeries.Points.Add(new DataPoint(mz - 0.0001, 0));
-                unannotatedSeries.Points.Add(new DataPoint(mz, intensity));
-                unannotatedSeries.Points.Add(new DataPoint(mz + 0.0001, 0));
-            }
-            Model.Series.Add(unannotatedSeries);
-        }
-
-        /// <summary>
-        /// Draws a peak on the spectrum
-        /// </summary>
-        /// <param name="mz">x value of peak to draw</param>
-        /// <param name="intensity">y max of peak to draw</param>
-        /// <param name="strokeWidth"></param>
-        /// <param name="color">Color to draw peak</param>
-        /// <param name="annotation">text to display above the peak</param>
-        protected void DrawPeak(double mz, double intensity, double strokeWidth, OxyColor color,
-            TextAnnotation annotation)
-        {
-            // peak line
-            var line = new LineSeries
-            {
-                Color = color,
-                StrokeThickness = strokeWidth
-            };
-            line.Points.Add(new DataPoint(mz, 0));
-            line.Points.Add(new DataPoint(mz, intensity));
-
-            // Miso is a tag used in chimeric ms1 plotting to indicate that we should not annotate this peak with a label. 
-            if (annotation != null && !annotation.Text.Contains("Miso"))
-            {
-                var x = annotation.TextPosition.X;
-                var y = annotation.TextPosition.Y + 20;
-                var splits = annotation.Text.Split('\n');
-
-                // Calculate y step for annotation lines based on Y-axis range
-                var yAxis = Model.Axes.FirstOrDefault(a => a.Position == AxisPosition.Left);
-                double yRange = yAxis != null ? Math.Abs(yAxis.ActualMaximum - yAxis.ActualMinimum) : 1.0;
-                double yStep = yRange * 0.05; // 5% of the y-range per line 
-
-                for (int j = splits.Length - 1; j >= 0; j--)
-                {
-                    var split = splits[j];
-                    var annotationLine = new TextAnnotation
-                    {
-                        Font = annotation.Font,
-                        FontSize = annotation.FontSize,
-                        FontWeight = annotation.FontWeight,
-                        TextColor = annotation.TextColor,
-                        StrokeThickness = annotation.StrokeThickness,
-                        Text = split,
-                        TextPosition = new DataPoint(x, y),
-                        TextVerticalAlignment = annotation.TextVerticalAlignment,
-                        TextHorizontalAlignment = HorizontalAlignment.Center
-                    };
-                    Model.Annotations.Add(annotationLine);
-                    y += yStep;
-                }
-            }
-
-            Model.Series.Add(line);
-        }
-
         /// <summary>
         /// Annotates all matched ion peaks
         /// </summary>
@@ -418,63 +282,6 @@ protected void ZoomAxes(IEnumerable<MatchedFragmentIon> matchedFramgentIons = nu
                 Model.Axes[0].Zoom(lowestAnnotatedMz - 100, highestAnnotatedMz + 100);
             }
         }
-
-        /// <summary>
-        /// Exports plot from a combined bitmap created in the children classes
-        /// </summary>
-        /// <param name="path"></param>
-        /// <param name="combinedBitmaps"></param>
-        /// <param name="width"></param>
-        /// <param name="height"></param>
-        public static void ExportPlot(string path, Bitmap combinedBitmaps, double width = 700, double height = 370)
-        {
-            width = width > 0 ? width : 700;
-            height = height > 0 ? height : 300;
-            switch (MetaDrawSettings.ExportType)
-            {
-                case "Pdf":
-                    string tempCombinedPath =
-                        System.IO.Path.Combine(System.IO.Path.GetDirectoryName(path), "tempCombined.png");
-                    combinedBitmaps.Save(tempCombinedPath, System.Drawing.Imaging.ImageFormat.Png);
-
-                    PdfDocument pdfDoc = new(new PdfWriter(path));
-                    Document document = new(pdfDoc,
-                        new iText.Kernel.Geom.PageSize((float)width - 30, (float)height - 30));
-
-                    ImageData sequenceAndLegendImageData = ImageDataFactory.Create(tempCombinedPath);
-                    iText.Layout.Element.Image sequenceAndPtmLegendImage = new(sequenceAndLegendImageData);
-                    sequenceAndPtmLegendImage.SetMarginLeft(-30);
-                    sequenceAndPtmLegendImage.SetMarginTop(-30);
-                    sequenceAndPtmLegendImage.ScaleToFit((float)width, (float)height);
-                    document.Add(sequenceAndPtmLegendImage);
-
-                    pdfDoc.Close();
-                    document.Close();
-                    File.Delete(tempCombinedPath);
-                    break;
-
-                case "Png":
-                    combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Png);
-                    break;
-
-                case "Jpeg":
-                    combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Jpeg);
-                    break;
-
-                case "Tiff":
-                    combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Tiff);
-                    break;
-
-                case "Wmf":
-                    combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Wmf);
-                    break;
-
-                case "Bmp":
-                    combinedBitmaps.Save(path, System.Drawing.Imaging.ImageFormat.Bmp);
-                    break;
-            }
-        }
-
         protected void AnnotateLibraryIons(bool isBetaPeptide, List<MatchedFragmentIon> libraryIons)
         {
             // figure out the sum of the intensities of the matched fragment ions
diff --git a/MetaMorpheus/GuiFunctions/MzLibExtensions.cs b/MetaMorpheus/GuiFunctions/MzLibExtensions.cs
index 227e4faea..e16796b98 100644
--- a/MetaMorpheus/GuiFunctions/MzLibExtensions.cs
+++ b/MetaMorpheus/GuiFunctions/MzLibExtensions.cs
@@ -47,11 +47,19 @@ public static bool IsCrossLinkedPeptide(this SpectrumMatchFromTsv sm)
 
         public static bool IsPeptide(this SpectrumMatchFromTsv sm)
         {
-            //if (sm is OsmFromTsv)
-            //    return false;
+            if (sm is OsmFromTsv)
+                return false;
             return true;
         }
 
+        public static string GetDigestionProductLabel(this SpectrumMatchFromTsv sm)
+        {
+            if (sm.IsPeptide())
+                return "Peptide";
+            else
+                return "Oligo";
+        }
+
         public static IBioPolymerWithSetMods ToBioPolymerWithSetMods(this SpectrumMatchFromTsv sm, string fullSequence = null)
         {
             //if (sm.IsPeptide())
@@ -79,5 +87,14 @@ public static bool MajorityWithin(this MzRange range, IEnumerable<double> values
             int within = values.Count(p => p >= range.Minimum && p <= range.Maximum);
             return within > values.Count() / 2;
         }
+
+        public static IEnumerable<(int Start, int End)> GetStartAndEndPosition(this SpectrumMatchFromTsv sm)
+        {
+            foreach (var ambigSplit in sm.StartAndEndResiduesInParentSequence.Split('|'))
+            {
+                var split = ambigSplit.Replace("[", "").Replace("]", "").Split("to");
+                yield return (int.Parse(split[0]), int.Parse(split[1]));
+            }
+        }
     }
 }
diff --git a/MetaMorpheus/GuiFunctions/Util/CyclicalQueue.cs b/MetaMorpheus/GuiFunctions/Util/CyclicalQueue.cs
new file mode 100644
index 000000000..5f8e970f0
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/Util/CyclicalQueue.cs
@@ -0,0 +1,33 @@
+using System;
+using System.Collections.Generic;
+
+namespace GuiFunctions.Util;
+
+public class CyclicalQueue<T>
+{
+    private readonly List<T> _items;
+    private int _index;
+
+    public CyclicalQueue(IEnumerable<T> items)
+    {
+        if (items == null) throw new ArgumentNullException(nameof(items));
+        _items = new List<T>(items);
+        if (_items.Count == 0)
+            throw new ArgumentException("CyclicalQueue must be initialized with at least one item.");
+        _index = 0;
+    }
+
+    public T Dequeue()
+    {
+        var item = _items[_index];
+        _index = (_index + 1) % _items.Count;
+        return item;
+    }
+
+    public void Reset()
+    {
+        _index = 0;
+    }
+
+    public int Count => _items.Count;
+}
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/BaseViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/BaseViewModel.cs
index 9c2933740..f2ed766c9 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/BaseViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/BaseViewModel.cs
@@ -26,7 +26,7 @@ public void OnPropertyChanged(string name)
 
         #region Helpers
 
-        protected string AddSpaces(string text)
+        protected static string AddSpaces(string text)
         {
             if (string.IsNullOrWhiteSpace(text))
                 return "";
@@ -41,7 +41,7 @@ protected string AddSpaces(string text)
             return newText.ToString();
         }
 
-        protected void AddSpaces(ObservableCollection<string> strings)
+        protected static void AddSpaces(ObservableCollection<string> strings)
         {
             for (int i = 0; i < strings.Count; i++)
             {
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/CoverageTypeForTreeViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/CoverageTypeForTreeViewModel.cs
index fdcdbc7ec..03976017f 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/CoverageTypeForTreeViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/CoverageTypeForTreeViewModel.cs
@@ -1,4 +1,5 @@
 using OxyPlot;
+using OxyPlot.Wpf;
 using System.Windows.Media;
 
 namespace GuiFunctions
@@ -47,6 +48,13 @@ public ColorForTreeViewModel(string name, OxyColor defaultColor)
             ColorBrush = DrawnSequence.ParseColorBrushFromOxyColor(defaultColor);
         }
 
+        public ColorForTreeViewModel(string name, SolidColorBrush brush)
+        {
+            Name = name;
+            ColorBrush = brush;
+            SelectedColor = AddSpaces(brush.ToOxyColor().GetColorName());
+        }
+
         #endregion
 
         public void SelectionChanged(string newColor)
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/LoadingProgressViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/LoadingProgressViewModel.cs
new file mode 100644
index 000000000..7fb7eb0a4
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/ViewModels/LoadingProgressViewModel.cs
@@ -0,0 +1,61 @@
+using System;
+using System.Collections.ObjectModel;
+
+namespace GuiFunctions;
+
+public class LoadingProgressViewModel : BaseViewModel
+{
+    private static readonly Lazy<LoadingProgressViewModel> _instance = new(() => new LoadingProgressViewModel());
+    public static LoadingProgressViewModel Instance => _instance.Value;
+
+    public ObservableCollection<LoadingStepViewModel> Steps { get; } = new();
+
+    private bool _isVisible;
+    public bool IsVisible
+    {
+        get => _isVisible;
+        set
+        {
+            if (_isVisible == value) return;
+            _isVisible = value;
+            OnPropertyChanged(nameof(IsVisible));
+        }
+    }
+
+    private LoadingProgressViewModel() { }
+}
+
+
+public class LoadingStepViewModel : BaseViewModel
+{
+    private int _current;
+    public int Current
+    {
+        get => _current;
+        set { _current = value; OnPropertyChanged(nameof(Current)); }
+    }
+
+    private int _total;
+    public int Total
+    {
+        get => _total;
+        set 
+        {
+            if (value == _total) return;
+            _total = value; 
+            OnPropertyChanged(nameof(Total)); 
+        }
+    }
+
+    private string _stepName;
+    public string StepName
+    {
+        get => _stepName;
+        set 
+        {
+            if (_stepName == value) return;
+            _stepName = value; 
+            OnPropertyChanged(nameof(StepName));
+        }
+    }
+}
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
index a35b50f4b..4ca71c732 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
@@ -29,6 +29,8 @@ public class MetaDrawSettingsViewModel : BaseViewModel, IAsyncInitialization
         private ObservableCollection<IonTypeForTreeViewModel> _IonGroups = new ObservableCollection<IonTypeForTreeViewModel>();
         private ObservableCollection<CoverageTypeForTreeViewModel> _CoverageColors = new ObservableCollection<CoverageTypeForTreeViewModel>();
         private ObservableCollection<ColorForTreeViewModel> _DataVisualizationColors = new ObservableCollection<ColorForTreeViewModel>();
+        private ObservableCollection<ColorForTreeViewModel> _BioPolymerCoverageColors = new ObservableCollection<ColorForTreeViewModel>();
+
         private bool _LoadedIons { get { return (_IonGroups.Count > 0); } }
         private bool _LoadedPTMs { get { return (_Modifications.Count > 0); } }
         private bool _LoadedSequenceCoverage { get { return (_CoverageColors.Count > 0); } }
@@ -246,6 +248,23 @@ public bool NormalizeHistogramToFile
             set { MetaDrawSettings.NormalizeHistogramToFile = value; OnPropertyChanged(nameof(NormalizeHistogramToFile)); }
         }
 
+        // BioPolymer Coverage Settings
+        public ObservableCollection<ColorForTreeViewModel> BioPolymerCoverageColors
+        {
+            get => _BioPolymerCoverageColors;
+            set
+            {
+                _BioPolymerCoverageColors = value;
+                OnPropertyChanged(nameof(BioPolymerCoverageColors));
+            }
+        }
+
+        public int BioPolymerCoverageFontSize
+        {
+            get => MetaDrawSettings.BioPolymerCoverageFontSize;
+            set { MetaDrawSettings.BioPolymerCoverageFontSize = value; OnPropertyChanged(nameof(BioPolymerCoverageFontSize)); }
+        }
+
         #endregion
 
         #region Constructor
@@ -272,6 +291,7 @@ internal MetaDrawSettingsViewModel(bool loadAsync = true)
                 LoadIonTypes();
                 LoadSequenceCoverage();
                 LoadDataVisualizationColors();
+                LoadBioPolymerCoverageColors();
                 Initialization = Task.CompletedTask;
             }
 
@@ -294,6 +314,7 @@ private async Task InitializeAsync()
             LoadIonTypes();
             LoadSequenceCoverage();
             LoadDataVisualizationColors();
+            LoadBioPolymerCoverageColors();
             await Task.Delay(100);
         }
 
@@ -351,6 +372,15 @@ public void Save()
                 if (color.HasChanged)
                     MetaDrawSettings.DataVisualizationColorOrder[i] = DrawnSequence.ParseOxyColorFromName(color.SelectedColor.Replace(" ", ""));
             }
+
+            foreach (var color in BioPolymerCoverageColors)
+            {
+                if (color.HasChanged)
+                {
+                    var key = Enum.Parse<BioPolymerCoverageType>(color.Name.Replace(" ", ""));
+                    MetaDrawSettings.BioPolymerCoverageColors[key] = color.ColorBrush;
+                }
+            }
         }
 
         /// <summary>
@@ -424,6 +454,14 @@ public void LoadDataVisualizationColors()
             }
         }
 
+        public void LoadBioPolymerCoverageColors()
+        {
+            foreach (var col in MetaDrawSettings.BioPolymerCoverageColors)
+            {
+                _BioPolymerCoverageColors.Add(new(AddSpaces(col.Key.ToString()), col.Value));
+            }
+        }
+
         #endregion
     }
 
diff --git a/MetaMorpheus/MetaMorpheus.sln.DotSettings b/MetaMorpheus/MetaMorpheus.sln.DotSettings
index ec69c7436..28c78fd7f 100644
--- a/MetaMorpheus/MetaMorpheus.sln.DotSettings
+++ b/MetaMorpheus/MetaMorpheus.sln.DotSettings
@@ -9,6 +9,7 @@
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=deadend/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Decon/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Deconvolute/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Deconvoluted/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=fasta/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Frac/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Glyco/@EntryIndexedValue">True</s:Boolean>
diff --git a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs
index 861bd145d..991de35f8 100644
--- a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs
+++ b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs
@@ -99,9 +99,7 @@ public abstract class MetaMorpheusTask
                     })))
             // Ignore all properties that are not user settable, instantiate with defaults. If the toml differs, defaults will be overridden. 
             .ConfigureType<ClassicDeconvolutionParameters>(type => type
-                .CreateInstance(() => new ClassicDeconvolutionParameters(1, 20, 4, 3))
-                .IgnoreProperty(p => p.IntensityRatioLimit)
-                .IgnoreProperty(p => p.DeconvolutionTolerancePpm))
+                .CreateInstance(() => new ClassicDeconvolutionParameters(1, 20, 4, 3)))
             .ConfigureType<IsoDecDeconvolutionParameters>(type => type
                 .CreateInstance(() => new IsoDecDeconvolutionParameters())
                 .IgnoreProperty(p => p.Verbose)
@@ -675,7 +673,7 @@ public MyTaskResults RunTask(string output_folder, List<DbForTask> currentProtei
 
         #region Database Loading
 
-        protected List<IBioPolymer> LoadBioPolymers(string taskId, List<DbForTask> dbFilenameList, bool searchTarget, DecoyType decoyType, List<string> localizeableModificationTypes, CommonParameters commonParameters)
+        public List<IBioPolymer> LoadBioPolymers(string taskId, List<DbForTask> dbFilenameList, bool searchTarget, DecoyType decoyType, List<string> localizeableModificationTypes, CommonParameters commonParameters)
         {
             Status($"Loading {GlobalVariables.AnalyteType.GetBioPolymerLabel()}s...", new List<string> { taskId });
             int emptyEntries = 0;
diff --git a/MetaMorpheus/Test/GuiTests/CyclicalQueueTests.cs b/MetaMorpheus/Test/GuiTests/CyclicalQueueTests.cs
new file mode 100644
index 000000000..78dd5c0bd
--- /dev/null
+++ b/MetaMorpheus/Test/GuiTests/CyclicalQueueTests.cs
@@ -0,0 +1,86 @@
+using GuiFunctions.Util;
+using NUnit.Framework;
+
+namespace Test.GuiTests;
+
+[TestFixture]
+public class CyclicalQueueTests
+{
+    [Test]
+    public void Constructor_ThrowsOnNull()
+    {
+        Assert.That(() => new CyclicalQueue<int>(null), Throws.ArgumentNullException);
+    }
+
+    [Test]
+    public void Constructor_ThrowsOnEmpty()
+    {
+        Assert.That(() => new CyclicalQueue<int>(new int[0]), Throws.ArgumentException);
+    }
+
+    [Test]
+    public void Constructor_WorksWithValidInput()
+    {
+        var queue = new CyclicalQueue<string>(new[] { "a", "b" });
+        Assert.That(queue.Count, Is.EqualTo(2));
+    }
+
+    [Test]
+    public void Dequeue_CyclesThroughAllItems()
+    {
+        var items = new[] { 1, 2, 3 };
+        var queue = new CyclicalQueue<int>(items);
+
+        Assert.That(queue.Dequeue(), Is.EqualTo(1));
+        Assert.That(queue.Dequeue(), Is.EqualTo(2));
+        Assert.That(queue.Dequeue(), Is.EqualTo(3));
+        // Should cycle back to start
+        Assert.That(queue.Dequeue(), Is.EqualTo(1));
+        Assert.That(queue.Dequeue(), Is.EqualTo(2));
+    }
+
+    [Test]
+    public void Reset_SetsIndexToZero()
+    {
+        var queue = new CyclicalQueue<string>(new[] { "x", "y" });
+        queue.Dequeue(); // "x"
+        queue.Dequeue(); // "y"
+        queue.Reset();
+        Assert.That(queue.Dequeue(), Is.EqualTo("x"));
+    }
+
+    [Test]
+    public void Count_ReturnsCorrectCount()
+    {
+        var queue = new CyclicalQueue<double>(new[] { 1.1, 2.2, 3.3 });
+        Assert.That(queue.Count, Is.EqualTo(3));
+    }
+
+    [Test]
+    public void Dequeue_OneItem_AlwaysReturnsThatItem()
+    {
+        var queue = new CyclicalQueue<int>(new[] { 42 });
+        Assert.That(queue.Dequeue(), Is.EqualTo(42));
+        Assert.That(queue.Dequeue(), Is.EqualTo(42));
+        Assert.That(queue.Dequeue(), Is.EqualTo(42));
+    }
+
+    [Test]
+    public static void Dequeue_ResetsOnCollectionBeingEmpty()
+    {
+        var queue = new CyclicalQueue<int>(new[] { 1, 2, 3 });
+        Assert.That(queue.Dequeue(), Is.EqualTo(1));
+        Assert.That(queue.Dequeue(), Is.EqualTo(2));
+        Assert.That(queue.Dequeue(), Is.EqualTo(3));
+
+        // Collection is now "empty" in the sense that we've cycled through all items
+        Assert.That(queue.Dequeue(), Is.EqualTo(1)); // Should reset and return first item
+        Assert.That(queue.Dequeue(), Is.EqualTo(2));
+        Assert.That(queue.Dequeue(), Is.EqualTo(3));
+
+
+        Assert.That(queue.Dequeue(), Is.EqualTo(1));
+        Assert.That(queue.Dequeue(), Is.EqualTo(2));
+        Assert.That(queue.Dequeue(), Is.EqualTo(3));
+    }   
+}
diff --git a/MetaMorpheus/Test/GuiTests/MzLibExtensionsTests.cs b/MetaMorpheus/Test/GuiTests/MzLibExtensionsTests.cs
index 37bcc1fc9..3d5cf8da8 100644
--- a/MetaMorpheus/Test/GuiTests/MzLibExtensionsTests.cs
+++ b/MetaMorpheus/Test/GuiTests/MzLibExtensionsTests.cs
@@ -1,9 +1,11 @@
 using System;
 using System.Collections.Generic;
+using System.IO;
 using GuiFunctions;
 using MassSpectrometry;
 using MzLibUtil;
 using NUnit.Framework;
+using Readers;
 using Assert = NUnit.Framework.Assert;
 
 namespace Test.GuiTests;
@@ -11,6 +13,20 @@ namespace Test.GuiTests;
 [TestFixture]
 public class MzLibExtensionsTests
 {
+    public PsmFromTsv TestPsm;
+    public OsmFromTsv TestOsm;
+
+    [OneTimeSetUp]
+    public void OneTimeSetUp()
+    {
+        string psmPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "SequenceCoverageTestPSM.psmtsv");
+        string osmPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Transcriptomics", "TestData" , "AllOligos.osmtsv");
+
+        TestPsm = SpectrumMatchTsvReader.ReadTsv<PsmFromTsv>(psmPath, out _)[0];
+        TestOsm = SpectrumMatchTsvReader.ReadTsv<OsmFromTsv>(osmPath, out _)[0];
+    }
+
+
     [Test]
     public void ToViewModel_WithClassicDeconvolutionParameters_ReturnsClassicDeconParamsViewModel()
     {
@@ -64,4 +80,55 @@ public void MajorityWithin_ReturnsFalse_WhenMajorityNotWithinRange()
         // Only 1 out of 5 is within [10, 20]
         Assert.That(range.MajorityWithin(values), Is.False);
     }
+    [Test]
+    public void IsPeptide_ReturnsTrue_ForPsmFromTsv()
+    {
+        // Arrange
+        var psm = TestPsm;
+
+        // Act
+        var result = psm.IsPeptide();
+
+        // Assert
+        Assert.That(result, Is.True);
+    }
+
+    [Test]
+    public void IsPeptide_ReturnsFalse_ForOsmFromTsv()
+    {
+        // Arrange
+        var osm = TestOsm;
+
+        // Act
+        var result = osm.IsPeptide();
+
+        // Assert
+        Assert.That(result, Is.False);
+    }
+
+    [Test]
+    public void GetDigestionProductLabel_ReturnsPeptide_ForPsmFromTsv()
+    {
+        // Arrange
+        var psm = TestPsm;
+
+        // Act
+        var label = psm.GetDigestionProductLabel();
+
+        // Assert
+        Assert.That(label, Is.EqualTo("Peptide"));
+    }
+
+    [Test]
+    public void GetDigestionProductLabel_ReturnsOligo_ForOsmFromTsv()
+    {
+        // Arrange
+        var osm = TestOsm;
+
+        // Act
+        var label = osm.GetDigestionProductLabel();
+
+        // Assert
+        Assert.That(label, Is.EqualTo("Oligo"));
+    }
 }
\ No newline at end of file
diff --git a/MetaMorpheus/Test/MetaDraw/BioPolymerCoverageMapViewModelTests.cs b/MetaMorpheus/Test/MetaDraw/BioPolymerCoverageMapViewModelTests.cs
new file mode 100644
index 000000000..f6a30f7b6
--- /dev/null
+++ b/MetaMorpheus/Test/MetaDraw/BioPolymerCoverageMapViewModelTests.cs
@@ -0,0 +1,263 @@
+using GuiFunctions.MetaDraw;
+using NUnit.Framework;
+using System.IO;
+using System.Linq;
+using System.Windows.Media;
+using Readers;
+using System.Threading;
+
+namespace Test.MetaDraw;
+
+[TestFixture]
+public class BioPolymerCoverageMapViewModelTests
+{
+    [Test]
+    public void LettersPerRow_Default_Is50()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        Assert.That(vm.LettersPerRow, Is.EqualTo(50));
+    }
+
+    [Test]
+    public void LettersPerRow_Setter_UpdatesValueAndRaisesPropertyChanged()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        bool propertyChanged = false;
+        vm.PropertyChanged += (s, e) => { if (e.PropertyName == nameof(vm.LettersPerRow)) propertyChanged = true; };
+        vm.LettersPerRow = 42;
+        Assert.That(vm.LettersPerRow, Is.EqualTo(42));
+        Assert.That(propertyChanged, Is.True);
+    }
+
+    [Test]
+    public void AvailableWidth_Default_Is800()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        Assert.That(vm.AvailableWidth, Is.EqualTo(800));
+    }
+
+    [Test]
+    public void AvailableWidth_Setter_UpdatesValueAndRaisesPropertyChanged()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        bool propertyChanged = false;
+        vm.PropertyChanged += (s, e) => { if (e.PropertyName == nameof(vm.AvailableWidth)) propertyChanged = true; };
+        vm.AvailableWidth = 1234;
+        Assert.That(vm.AvailableWidth, Is.EqualTo(1234));
+        Assert.That(propertyChanged, Is.True);
+    }
+
+    [Test]
+    public void UpdateLettersPerRow_ChangesLettersPerRow_WhenWidthChanges()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        int before = vm.LettersPerRow;
+        vm.UpdateLettersPerRow(2000);
+        Assert.That(vm.LettersPerRow, Is.Not.EqualTo(before));
+    }
+
+    [Test]
+    public void UpdateLettersPerRow_DoesNotSetBelow10()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        vm.UpdateLettersPerRow(1); // very small width
+        Assert.That(vm.LettersPerRow, Is.EqualTo(10));
+    }
+
+    [Test]
+    public void UpdateLettersPerRow_CallsRedraw_IfLettersPerRowUnchanged()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        bool redrawCalled = false;
+        // Use reflection to replace private Redraw with a test hook
+        var method = typeof(BioPolymerCoverageMapViewModel).GetMethod("Redraw", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+        Assert.That(method, Is.Not.Null);
+        // Set LettersPerRow to a known value
+        vm.LettersPerRow = 20;
+        // Now call UpdateLettersPerRow with a width that results in the same LettersPerRow
+        double width = 20 * 16 * 0.70; // assuming font size 16
+        // Can't directly hook Redraw, but we can set Group and check CoverageDrawing is not null after
+        var match = new DummySpectralmatch(0.01, "1", "f.psmtsv");
+        var results = new[] { new BioPolymerCoverageResultModel(match, "ABC", 1, 2, BioPolymerCoverageType.Unique) };
+        var group = new BioPolymerGroupViewModel("ACC", "Prot", "ABC", results);
+        vm.Group = group;
+        var beforeDrawing = vm.CoverageDrawing;
+        vm.UpdateLettersPerRow(width);
+        Assert.That(vm.CoverageDrawing, Is.Not.Null);
+    }
+
+    [Test]
+    public void ColorBy_Setter_UpdatesValue_ClearsColors_RaisesPropertyChanged()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        bool propertyChanged = false;
+        vm.PropertyChanged += (s, e) => { if (e.PropertyName == nameof(vm.ColorBy)) propertyChanged = true; };
+
+        // Set to FileOrigin from default CoverageType
+        vm.ColorBy = ColorResultsBy.FileOrigin;
+        Assert.That(vm.ColorBy, Is.EqualTo(ColorResultsBy.FileOrigin));
+        Assert.That(propertyChanged, Is.True);
+
+        // Set to None, should also update
+        propertyChanged = false;
+        vm.ColorBy = ColorResultsBy.None;
+        Assert.That(vm.ColorBy, Is.EqualTo(ColorResultsBy.None));
+        Assert.That(propertyChanged, Is.True);
+    }
+
+    [Test]
+    public void Plotting_WithColorByFileOrigin_AssignsDistinctColorsAndLegendItems()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        vm.ColorBy = ColorResultsBy.FileOrigin;
+
+        // Create two results from different files
+        var match1 = new DummySpectralmatch(0.005, "1", "fileA.psmtsv");
+        var match2 = new DummySpectralmatch(0.01, "2", "fileB.psmtsv");
+        var result1 = new BioPolymerCoverageResultModel(match1, "ABC", 1, 2, BioPolymerCoverageType.Unique);
+        var result2 = new BioPolymerCoverageResultModel(match2, "ABC", 2, 3, BioPolymerCoverageType.Unique);
+
+        var group = new BioPolymerGroupViewModel("ACC", "Prot", "ABC", new[] { result1, result2 });
+        vm.Group = group;
+
+        // After setting Group, CoverageDrawing should be non-null
+        Assert.That(vm.CoverageDrawing, Is.Not.Null);
+
+        // Use reflection to access the private IdentifierToColor dictionary
+        var idToColorField = typeof(BioPolymerCoverageMapViewModel)
+            .GetField("IdentifierToColor", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Static);
+        Assert.That(idToColorField, Is.Not.Null);
+
+        var idToColor = idToColorField.GetValue(null) as System.Collections.IDictionary;
+        Assert.That(idToColor, Is.Not.Null);
+
+        // Both file names should be present and mapped to SolidColorBrush
+        Assert.That(idToColor.Contains("fileA.psmtsv"), Is.True);
+        Assert.That(idToColor.Contains("fileB.psmtsv"), Is.True);
+        var brushA = idToColor["fileA.psmtsv"] as SolidColorBrush;
+        var brushB = idToColor["fileB.psmtsv"] as SolidColorBrush;
+        Assert.That(brushA, Is.Not.Null);
+        Assert.That(brushB, Is.Not.Null);
+        Assert.That(brushA.Color, Is.Not.EqualTo(brushB.Color));
+
+        // Legend items should include both files
+        // Use reflection to call private CreateLegendItems
+        var method = typeof(BioPolymerCoverageMapViewModel)
+            .GetMethod("CreateLegendItems", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+        Assert.That(method, Is.Not.Null);
+
+        var filteredResults = group.CoverageResults.ToList();
+        double fontSize = 16; // typical font size
+        double dpi = 96; // typical DPI
+        var legendItems = method.Invoke(vm, new object[] { filteredResults, fontSize, dpi, ColorResultsBy.FileOrigin }) as System.Collections.IEnumerable;
+        Assert.That(legendItems, Is.Not.Null);
+
+        var legendLabels = legendItems.Cast<(SolidColorBrush Brush, System.Windows.Media.FormattedText Text)>().Select(li => li.Text.Text).ToList();
+        Assert.That(legendLabels.Any(l => l.Contains("fileA.psmtsv")), Is.True);
+        Assert.That(legendLabels.Any(l => l.Contains("fileB.psmtsv")), Is.True);
+    }
+
+    [Test]
+    public void Plotting_WithColorByCoverageType_AssignsTypeColorsAndLegendItems()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        vm.ColorBy = ColorResultsBy.CoverageType;
+
+        // Create two results with different coverage types
+        var match1 = new DummySpectralmatch(0.005, "1", "fileA.psmtsv");
+        var match2 = new DummySpectralmatch(0.01, "2", "fileB.psmtsv");
+        var result1 = new BioPolymerCoverageResultModel(match1, "ABC", 1, 2, BioPolymerCoverageType.Unique);
+        var result2 = new BioPolymerCoverageResultModel(match2, "ABC", 2, 3, BioPolymerCoverageType.Shared);
+
+        var group = new BioPolymerGroupViewModel("ACC", "Prot", "ABC", new[] { result1, result2 });
+        vm.Group = group;
+
+        // After setting Group, CoverageDrawing should be non-null
+        Assert.That(vm.CoverageDrawing, Is.Not.Null);
+
+        // Legend items should include both coverage types
+        var method = typeof(BioPolymerCoverageMapViewModel)
+            .GetMethod("CreateLegendItems", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+        Assert.That(method, Is.Not.Null);
+
+        var filteredResults = group.CoverageResults.ToList();
+        double fontSize = 16; // typical font size
+        double dpi = 96; // typical DPI
+        var legendItems = method.Invoke(vm, new object[] { filteredResults, fontSize, dpi, ColorResultsBy.CoverageType }) as System.Collections.IEnumerable;
+        Assert.That(legendItems, Is.Not.Null);
+
+        var legendLabels = legendItems.Cast<(SolidColorBrush Brush, System.Windows.Media.FormattedText Text)>().Select(li => li.Text.Text).ToList();
+        Assert.That(legendLabels.Any(l => l.Contains("Unique")), Is.True);
+        Assert.That(legendLabels.Any(l => l.Contains("Shared")), Is.True);
+
+        // The brushes should be the ones from MetaDrawSettings.BioPolymerCoverageColors
+        var brushes = legendItems.Cast<(SolidColorBrush Brush, System.Windows.Media.FormattedText Text)>().Select(li => li.Brush).ToList();
+        Assert.That(brushes.Distinct().Count(), Is.EqualTo(2));
+    }
+
+    [Test]
+    public void Plotting_WithColorByNone_AssignsGrayColorAndNoLegendItems()
+    {
+        var vm = new BioPolymerCoverageMapViewModel();
+        vm.ColorBy = ColorResultsBy.None;
+
+        // Create two results with different coverage types and files
+        var match1 = new DummySpectralmatch(0.005, "1", "fileA.psmtsv");
+        var match2 = new DummySpectralmatch(0.01, "2", "fileB.psmtsv");
+        var result1 = new BioPolymerCoverageResultModel(match1, "ABC", 1, 2, BioPolymerCoverageType.Unique);
+        var result2 = new BioPolymerCoverageResultModel(match2, "ABC", 2, 3, BioPolymerCoverageType.Shared);
+
+        var group = new BioPolymerGroupViewModel("ACC", "Prot", "ABC", new[] { result1, result2 });
+        vm.Group = group;
+
+        // After setting Group, CoverageDrawing should be non-null
+        Assert.That(vm.CoverageDrawing, Is.Not.Null);
+
+        // Legend items should be empty
+        var method = typeof(BioPolymerCoverageMapViewModel)
+            .GetMethod("CreateLegendItems", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+        Assert.That(method, Is.Not.Null);
+
+        var filteredResults = group.CoverageResults.ToList();
+        double fontSize = 16; // typical font size
+        double dpi = 96; // typical DPI
+        var legendItems = method.Invoke(vm, new object[] { filteredResults, fontSize, dpi, ColorResultsBy.None }) as System.Collections.IEnumerable;
+        Assert.That(legendItems, Is.Not.Null);
+        Assert.That(legendItems.Cast<object>().Any(), Is.False);
+    }
+
+    [Test]
+    public void Plotting_WithRealData()
+    {
+        // Bring in search results
+        if (!EverythingRunnerEngineTestCase.TryGetTestCase(EverythingRunnerEngineTestCases.BottomUpQValue, out var searchTestCase))
+            Assert.Fail();
+
+        var dbPath = searchTestCase.DatabaseList.First().FilePath;
+        var smPath = Directory.GetFiles(searchTestCase.OutputDirectory, "*PSMs.psmtsv", SearchOption.AllDirectories).First();
+        var matches = SpectrumMatchTsvReader.ReadTsv(smPath, out _);
+
+        // Load search results into Tab
+        var logic = new DummyMetaDrawLogic();
+        logic.AllSpectralMatches = matches;
+        logic.FilterPsms();
+
+        var tabVm = new BioPolymerTabViewModel(logic);
+        tabVm.DatabasePath = dbPath;
+        var method = typeof(BioPolymerTabViewModel)
+            .GetMethod("LoadDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+        method.Invoke(tabVm, null);
+        Thread.Sleep(1000); // wait for async load
+        Assert.That(tabVm.IsDatabaseLoaded, Is.True);
+
+        // Plot every group
+        var previous = tabVm.CoverageMapViewModel.CoverageDrawing;
+        foreach (var group in tabVm.AllGroups)
+        {
+            tabVm.SelectedGroup = group;
+            var current = tabVm.CoverageMapViewModel.CoverageDrawing;
+            Assert.That(current, Is.Not.Null);
+            Assert.That(current, Is.Not.EqualTo(previous));
+        }
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/Test/MetaDraw/BioPolymerCoverageResultModelTests.cs b/MetaMorpheus/Test/MetaDraw/BioPolymerCoverageResultModelTests.cs
new file mode 100644
index 000000000..1c31c03cf
--- /dev/null
+++ b/MetaMorpheus/Test/MetaDraw/BioPolymerCoverageResultModelTests.cs
@@ -0,0 +1,125 @@
+using System.Collections.Generic;
+using NUnit.Framework;
+using GuiFunctions;
+using GuiFunctions.MetaDraw;
+using Readers;
+
+namespace Test.MetaDraw;
+
+public class DummySpectralmatch : SpectrumMatchFromTsv
+{
+    public DummySpectralmatch(double qValue = 0.05, string ambiguity = "3", string filePath = "file1.psmtsv",  string accession = "ACC", string baseSeq = "ABC", string missedCleavages = "0", string startAndEnd = "[1 to 3]") 
+        : base("20100723_Velos1_TaGe_SA_Gamg_2-calib-averaged\t37933\t165.90394\t200.00000\t505630.47644\t37925\t3.00000\t151816.23307\t1194.56112\t3580.66153\t44.328\t39.328\t0\tGGGGGGGGGGGLGGGLGNVLGGLISGAGGGGGGGGGGGGGGGGGGGGTAMR\tGGGGGGGGGGGLGGGLGNVLGGLISGAGGGGGGGGGGGGGGGGGGGGTAMR\tGGGGGGGGGGGLGGGLGNVLGGLISGAGGGGGGGGGGGGGGGGGGGGTAMR\t1\t5\t\t\t\t0\t0\t3580.65338\t0.00815\t2.28000\tP04632\tCalpain small subunit 1\tprimary:CAPNS1, synonym:CAPN4, synonym:CAPNS\tHomo sapiens\t\t\tN\tN\tfull\t[10 to 60]\tK\tI\t \tT\t[y1+1, y2+1, y3+1, y4+1, y5+1, y6+1, y7+1, y8+1, y9+1, y10+1, y11+1, y12+1, y13+1, y14+1, y15+1, y16+1, y17+1, y18+1, y19+1, y20+1, y21+1, y22+1, y23+1, y24+1, y25+1, y26+1, y27+1, y28+1];[b2+1, b3+1, b4+1, b5+1, b6+1, b7+1, b8+1, b9+1, b10+1, b11+1, b12+1, b13+1, b14+1, b15+1, b16+1, b18+1]\t[y1+1:175.11889, y2+1:306.15954, y3+1:377.19654, y4+1:478.24453, y5+1:535.26597, y6+1:592.28604, y7+1:649.30788, y8+1:706.32920, y9+1:763.35010, y10+1:820.37208, y11+1:877.39447, y12+1:934.41413, y13+1:991.43748, y14+1:1048.45701, y15+1:1105.47696, y16+1:1162.50121, y17+1:1219.52228, y18+1:1276.53952, y19+1:1333.56720, y20+1:1390.58477, y21+1:1447.60893, y22+1:1504.63266, y23+1:1561.64614, y24+1:1618.67260, y25+1:1689.70263, y26+1:1746.72044, y27+1:1833.76364, y28+1:1946.83155];[b2+1:115.04997, b3+1:172.07162, b4+1:229.09313, b5+1:286.11466, b6+1:343.13611, b7+1:400.15770, b8+1:457.17939, b9+1:514.20071, b10+1:571.22127, b11+1:628.24464, b12+1:741.32787, b13+1:798.34733, b14+1:855.36264, b15+1:912.38839, b16+1:1025.47895, b18+1:1196.54361]\t[y1+1:-0.00006, y2+1:0.00010, y3+1:-0.00001, y4+1:0.00030, y5+1:0.00028, y6+1:-0.00112, y7+1:-0.00074, y8+1:-0.00088, y9+1:-0.00145, y10+1:-0.00093, y11+1:-0.00000, y12+1:-0.00181, y13+1:0.00008, y14+1:-0.00186, y15+1:-0.00337, y16+1:-0.00058, y17+1:-0.00097, y18+1:-0.00520, y19+1:0.00101, y20+1:-0.00288, y21+1:-0.00018, y22+1:0.00208, y23+1:-0.00590, y24+1:-0.00090, y25+1:-0.00799, y26+1:-0.01164, y27+1:-0.00047, y28+1:-0.01663];[b2+1:-0.00023, b3+1:-0.00004, b4+1:-0.00000, b5+1:0.00007, b6+1:0.00005, b7+1:0.00018, b8+1:0.00040, b9+1:0.00026, b10+1:-0.00064, b11+1:0.00126, b12+1:0.00043, b13+1:-0.00157, b14+1:-0.00773, b15+1:-0.00344, b16+1:0.00305, b18+1:0.00333]\t[y1+1:-0.37, y2+1:0.33, y3+1:-0.02, y4+1:0.62, y5+1:0.52, y6+1:-1.89, y7+1:-1.14, y8+1:-1.25, y9+1:-1.90, y10+1:-1.14, y11+1:-0.00, y12+1:-1.94, y13+1:0.08, y14+1:-1.78, y15+1:-3.05, y16+1:-0.50, y17+1:-0.80, y18+1:-4.08, y19+1:0.76, y20+1:-2.07, y21+1:-0.12, y22+1:1.38, y23+1:-3.78, y24+1:-0.56, y25+1:-4.73, y26+1:-6.67, y27+1:-0.26, y28+1:-8.54];[b2+1:-2.03, b3+1:-0.26, b4+1:-0.02, b5+1:0.24, b6+1:0.14, b7+1:0.45, b8+1:0.89, b9+1:0.51, b10+1:-1.13, b11+1:2.01, b12+1:0.58, b13+1:-1.97, b14+1:-9.04, b15+1:-3.78, b16+1:2.98, b18+1:2.78]\t[y1+1:9775, y2+1:1858, y3+1:3049, y4+1:1076, y5+1:1476, y6+1:2977, y7+1:3453, y8+1:3289, y9+1:3932, y10+1:4650, y11+1:4428, y12+1:4487, y13+1:4638, y14+1:4270, y15+1:4701, y16+1:5381, y17+1:3626, y18+1:3552, y19+1:2672, y20+1:2941, y21+1:2807, y22+1:2851, y23+1:2541, y24+1:6153, y25+1:1475, y26+1:2602, y27+1:5708, y28+1:888];[b2+1:2509, b3+1:8489, b4+1:9065, b5+1:8360, b6+1:7417, b7+1:4225, b8+1:4917, b9+1:3361, b10+1:2780, b11+1:3262, b12+1:2070, b13+1:1145, b14+1:908, b15+1:3497, b16+1:932, b18+1:1424]\t44\t0.5968\t \t \t1\t0\t0.000019\t1\t0\t0.000019\t0.00015681982040405273\t5.9E-05\r", ['\t'], HeaderToIndex)
+    {
+        QValue = qValue;
+        AmbiguityLevel = ambiguity;
+        FileNameWithoutExtension = filePath;
+        Accession = accession;
+        BaseSeq = baseSeq;
+        MissedCleavage = missedCleavages;
+        StartAndEndResiduesInParentSequence = startAndEnd;
+    }
+
+    // Header to ensure constructor runs. 
+    public static Dictionary<string, int> HeaderToIndex = new Dictionary<string, int>
+    {
+        { "File Name", 0 },
+        { "Scan Number", 1 },
+        { "Scan Retention Time", 2 },
+        { "Num Experimental Peaks", 3 },
+        { "Total Ion Current", 4 },
+        { "Precursor Scan Number", 5 },
+        { "Precursor Charge", 6 },
+        { "Precursor Intensity", 7 },
+        { "Precursor MZ", 8 },
+        { "Precursor Mass", 9 },
+        { "Score", 10 },
+        { "Delta Score", 11 },
+        { "Notch", 12 },
+        { "Base Sequence", 13 },
+        { "Full Sequence", 14 },
+        { "Essential Sequence", 15 },
+        { "Ambiguity Level", 16 },
+        { "PSM Count (unambiguous, <0.01 q-value)", 17 },
+        { "Mods", 18 },
+        { "Mods Chemical Formulas", 19 },
+        { "Mods Combined Chemical Formula", 20 },
+        { "Num Variable Mods", 21 },
+        { "Missed Cleavages", 22 },
+        { "Monoisotopic Mass", 23 },
+        { "Mass Diff (Da)", 24 },
+        { "Mass Diff (ppm)", 25 },
+        { "Accession", 26 },
+        { "Name", 27 },
+        { "Gene Name", 28 },
+        { "Organism Name", 29 },
+        { "Identified Sequence Variations", 30 },
+        { "Splice Sites", 31 },
+        { "Contaminant", 32 },
+        { "Decoy", 33 },
+        { "Description", 34 },
+        { "Start and End Residues In Full Sequence", 35 },
+        { "Previous Residue", 36 },
+        { "Next Residue", 37 },
+        { "Theoreticals Searched", 38 },
+        { "Decoy/Contaminant/Target", 39 },
+        { "Matched Ion Series", 40 },
+        { "Matched Ion Mass-To-Charge Ratios", 41 },
+        { "Matched Ion Mass Diff (Da)", 42 },
+        { "Matched Ion Mass Diff (Ppm)", 43 },
+        { "Matched Ion Intensities", 44 },
+        { "Matched Ion Counts", 45 },
+        { "Normalized Spectral Angle", 46 },
+        { "Localized Scores", 47 },
+        { "Improvement Possible", 48 },
+        { "Cumulative Target", 49 },
+        { "Cumulative Decoy", 50 },
+        { "QValue", 51 },
+        { "Cumulative Target Notch", 52 },
+        { "Cumulative Decoy Notch", 53 },
+        { "QValue Notch", 54 },
+        { "PEP", 55 },
+        { "PEP_QValue", 56 },
+        { "Intersecting Sequence Variations", -1 },
+        { "1/K0", -1 },
+        { "Intersectings", -1 },
+
+    };
+
+    // Dont use these, they will crash. 
+    public DummySpectralmatch(string line, char[] split, Dictionary<string, int> parsedHeader) : base(line, split, parsedHeader)
+    { 
+    }
+
+    public DummySpectralmatch(SpectrumMatchFromTsv psm, string fullSequence, int index = 0, string baseSequence = "") : base(psm, fullSequence, index, baseSequence)
+    {
+    }
+}
+
+[TestFixture]
+public class BioPolymerCoverageResultModelTests
+{
+    [Test]
+    public void Constructor_SetsProperties()
+    {
+        var match = new DummySpectralmatch();
+        var model = new BioPolymerCoverageResultModel(match, "SEQ", 2, 5, BioPolymerCoverageType.UniqueMissedCleavage);
+
+        Assert.That(model.Match, Is.EqualTo(match));
+        Assert.That(model.BaseSequence, Is.EqualTo("SEQ"));
+        Assert.That(model.Start, Is.EqualTo(2));
+        Assert.That(model.End, Is.EqualTo(5));
+        Assert.That(model.CoverageType, Is.EqualTo(BioPolymerCoverageType.UniqueMissedCleavage));
+    }
+
+    [Test]
+    public void Properties_DelegateToMatch()
+    {
+        var match = new DummySpectralmatch();
+        var model = new BioPolymerCoverageResultModel(match, "SEQ", 1, 3, BioPolymerCoverageType.Shared);
+
+        Assert.That(model.QValue, Is.EqualTo(0.05));
+        Assert.That(model.Ambiguity, Is.EqualTo("3"));
+        Assert.That(model.FileName, Is.EqualTo("file1.psmtsv"));
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/Test/MetaDraw/BioPolymerGroupViewModelTests.cs b/MetaMorpheus/Test/MetaDraw/BioPolymerGroupViewModelTests.cs
new file mode 100644
index 000000000..42310f3c6
--- /dev/null
+++ b/MetaMorpheus/Test/MetaDraw/BioPolymerGroupViewModelTests.cs
@@ -0,0 +1,55 @@
+using GuiFunctions;
+using GuiFunctions.MetaDraw;
+using NUnit.Framework;
+
+namespace Test.MetaDraw;
+
+[TestFixture]
+public class BioPolymerGroupViewModelTests
+{
+    [Test]
+    public void Constructor_InitializesProperties()
+    {
+        var match = new DummySpectralmatch(0.01, "1", "f.psmtsv");
+        var results = new[]
+        {
+            new BioPolymerCoverageResultModel(match, "ABC", 1, 2, BioPolymerCoverageType.Unique),
+            new BioPolymerCoverageResultModel(match, "ABC", 2, 3, BioPolymerCoverageType.Shared)
+        };
+        var group = new BioPolymerGroupViewModel("ACC", "Prot", "ABC", results);
+
+        Assert.That(group.Accession, Is.EqualTo("ACC"));
+        Assert.That(group.ProteinName, Is.EqualTo("Prot"));
+        Assert.That(group.Sequence, Is.EqualTo("ABC"));
+        Assert.That(group.Length, Is.EqualTo(3));
+        Assert.That(group.CoverageResults.Count, Is.EqualTo(2));
+    }
+
+    [Test]
+    public void UpdatePropertiesAfterFilter_ComputesCoverage()
+    {
+        var match = new DummySpectralmatch(0.01, "1", "f.psmtsv");
+        var results = new[]
+        {
+            new BioPolymerCoverageResultModel(match, "ABC", 1, 2, BioPolymerCoverageType.Unique),
+            new BioPolymerCoverageResultModel(match, "ABC", 2, 3, BioPolymerCoverageType.UniqueMissedCleavage),
+            new BioPolymerCoverageResultModel(match, "ABC", 1, 3, BioPolymerCoverageType.Shared)
+        };
+        var group = new BioPolymerGroupViewModel("ACC", "Prot", "ABC", results);
+        group.UpdatePropertiesAfterFilter();
+
+        Assert.That(group.GroupCount, Is.EqualTo(3));
+        Assert.That(group.UniqueSequenceCoverage, Is.GreaterThan(0));
+        Assert.That(group.MaximumSequenceCoverage, Is.EqualTo(1.0));
+    }
+
+    [Test]
+    public void UpdatePropertiesAfterFilter_EmptyResults()
+    {
+        var group = new BioPolymerGroupViewModel("ACC", "Prot", "ABC", new BioPolymerCoverageResultModel[0]);
+        group.UpdatePropertiesAfterFilter();
+        Assert.That(group.GroupCount, Is.EqualTo(0));
+        Assert.That(group.UniqueSequenceCoverage, Is.EqualTo(0));
+        Assert.That(group.MaximumSequenceCoverage, Is.EqualTo(0));
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/Test/MetaDraw/BioPolymerTabViewModelTests.cs b/MetaMorpheus/Test/MetaDraw/BioPolymerTabViewModelTests.cs
new file mode 100644
index 000000000..5009ad5e3
--- /dev/null
+++ b/MetaMorpheus/Test/MetaDraw/BioPolymerTabViewModelTests.cs
@@ -0,0 +1,483 @@
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Threading;
+using System.Windows.Media;
+using GuiFunctions;
+using GuiFunctions.MetaDraw;
+using NUnit.Framework;
+using Omics;
+using Proteomics;
+using Readers;
+
+namespace Test.MetaDraw
+{
+    public class DummyMetaDrawLogic : MetaDrawLogic
+    {
+        public DummyMetaDrawLogic()
+        {
+            AllSpectralMatches = new List<Readers.SpectrumMatchFromTsv>();
+        }
+    }
+
+    [TestFixture]
+    public class BioPolymerTabViewModelTests
+    {
+        private class DummyBioPolymer(string accession, string name, string baseSeq)
+            : Protein(baseSeq, accession, name: name);
+
+        [Test]
+        public void Constructor_InitializesProperties()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic, "C:\\Export");
+            Assert.That(vm.AllGroups, Is.Not.Null);
+            Assert.That(vm.FilteredGroups, Is.Not.Null);
+            Assert.That(vm.CoverageMapViewModel, Is.Not.Null);
+            Assert.That(vm.ExportDirectory, Is.EqualTo("C:\\Export"));
+            Assert.That(vm.LoadDatabaseCommand, Is.Not.Null);
+            Assert.That(vm.ResetDatabaseCommand, Is.Not.Null);
+            Assert.That(vm.ExportImageCommand, Is.Not.Null);
+        }
+
+        [Test]
+        public void IsDatabaseLoaded_PropertyChanged()
+        {
+            var vm = new BioPolymerTabViewModel(new DummyMetaDrawLogic());
+            bool called = false;
+            vm.PropertyChanged += (s, e) => { if (e.PropertyName == "IsDatabaseLoaded") called = true; };
+            vm.IsDatabaseLoaded = true;
+            Assert.That(vm.IsDatabaseLoaded, Is.True);
+            Assert.That(called, Is.True);
+        }
+
+        [Test]
+        public void DatabasePath_And_DatabaseName_PropertyChanged()
+        {
+            var vm = new BioPolymerTabViewModel(new DummyMetaDrawLogic());
+            bool pathChanged = false, nameChanged = false;
+            vm.PropertyChanged += (s, e) =>
+            {
+                if (e.PropertyName == "DatabasePath") pathChanged = true;
+                if (e.PropertyName == "DatabaseName") nameChanged = true;
+            };
+            vm.DatabasePath = "C:\\db.fasta";
+            Assert.That(vm.DatabasePath, Is.EqualTo("C:\\db.fasta"));
+            Assert.That(vm.DatabaseName, Is.Not.Null.And.Not.Empty);
+            Assert.That(pathChanged, Is.True);
+            Assert.That(nameChanged, Is.True);
+        }
+
+        [Test]
+        public void SearchText_PropertyChanged_And_FilteredGroups()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            var group1 = new BioPolymerGroupViewModel("A1", "Alpha", "ABC", new BioPolymerCoverageResultModel[0]);
+            var group2 = new BioPolymerGroupViewModel("B2", "Beta", "DEF", new BioPolymerCoverageResultModel[0]);
+            vm.AllGroups.Add(group1);
+            vm.AllGroups.Add(group2);
+
+            bool changed = false;
+            vm.PropertyChanged += (s, e) => { if (e.PropertyName == "SearchText") changed = true; };
+
+            vm.SearchText = "Alpha";
+            Assert.That(changed, Is.True);
+            Assert.That(vm.FilteredGroups.Count, Is.EqualTo(1));
+            Assert.That(vm.FilteredGroups[0], Is.EqualTo(group1));
+
+            vm.SearchText = "B2";
+            Assert.That(vm.FilteredGroups.Count, Is.EqualTo(1));
+            Assert.That(vm.FilteredGroups[0], Is.EqualTo(group2));
+
+            vm.SearchText = "";
+            Assert.That(vm.FilteredGroups.Count, Is.EqualTo(2));
+        }
+
+        [Test]
+        public void SelectedGroup_PropertyChanged_And_CoverageMapViewModel()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            var group = new BioPolymerGroupViewModel("A1", "Alpha", "ABC", new BioPolymerCoverageResultModel[0]);
+            bool changed = false;
+            vm.PropertyChanged += (s, e) => { if (e.PropertyName == "SelectedGroup") changed = true; };
+            vm.SelectedGroup = group;
+            Assert.That(vm.SelectedGroup, Is.EqualTo(group));
+            Assert.That(vm.CoverageMapViewModel.Group, Is.EqualTo(group));
+            Assert.That(changed, Is.True);
+        }
+
+        [Test]
+        public void ResetDatabase_ClearsState()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            vm.DatabasePath = "C:\\db.fasta";
+            vm.DatabaseName = "db";
+            vm.AllGroups.Add(new BioPolymerGroupViewModel("A1", "Alpha", "ABC", new BioPolymerCoverageResultModel[0]));
+            vm.FilteredGroups.Add(new BioPolymerGroupViewModel("B2", "Beta", "DEF", new BioPolymerCoverageResultModel[0]));
+
+            vm.GetType().GetMethod("ResetDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+                .Invoke(vm, null);
+
+            Assert.That(vm.DatabasePath, Is.Empty);
+            Assert.That(vm.DatabaseName, Is.Empty);
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(0));
+            Assert.That(vm.FilteredGroups.Count, Is.EqualTo(0));
+        }
+
+        [Test]
+        public void ExportDirectory_CreatesDirectoryIfNotExists()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var tempDir = System.IO.Path.Combine(System.IO.Path.GetTempPath(), "BioPolymerTabViewModelTestDir");
+            if (System.IO.Directory.Exists(tempDir))
+                System.IO.Directory.Delete(tempDir, true);
+
+            var vm = new BioPolymerTabViewModel(logic, tempDir);
+            bool changed = false;
+            vm.PropertyChanged += (s, e) => { if (e.PropertyName == "ExportDirectory") changed = true; };
+            var dir = vm.ExportDirectory;
+            Assert.That(System.IO.Directory.Exists(dir), Is.True);
+            Assert.That(changed, Is.False); // Only fires on set, not get
+
+            vm.ExportDirectory = tempDir + "2";
+            Assert.That(vm.ExportDirectory, Is.EqualTo(tempDir + "2"));
+            Assert.That(changed, Is.True);
+
+            System.IO.Directory.Delete(tempDir, true);
+            if (System.IO.Directory.Exists(tempDir + "2"))
+                System.IO.Directory.Delete(tempDir + "2", true);
+        }
+
+        [Test]
+        public void ProcessSpectralMatches_AddsGroups()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+
+            // Setup _allBioPolymers with a dummy
+            var dummyBioPolymer = new DummyBioPolymer("ACC", "Protein", "ABC");
+            var allBioPolymersField = typeof(BioPolymerTabViewModel).GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            allBioPolymersField.SetValue(vm, new Dictionary<string, IBioPolymer> { { "ACC", dummyBioPolymer } });
+
+            var match = new DummySpectralmatch();
+            var matches = new List<Readers.SpectrumMatchFromTsv> { match };
+            vm.ProcessSpectralMatches(matches);
+
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(1));
+            Assert.That(vm.AllGroups[0].Accession, Is.EqualTo("ACC"));
+        }
+
+        [Test]
+        public void LoadDatabase_DoesNothing_WhenPathIsNullOrEmpty()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            
+            var allBioPolymersField = typeof(BioPolymerTabViewModel)
+                .GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            allBioPolymersField.SetValue(vm, new Dictionary<string, IBioPolymer>());
+            var method = typeof(BioPolymerTabViewModel)
+                .GetMethod("LoadDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            method.Invoke(vm, null);
+            Assert.That(vm.IsDatabaseLoaded, Is.False);
+        }
+
+        [Test]
+        public void LoadDatabase_CatchesException_AndDoesNotThrow()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            // Set an invalid path to force exception
+            vm.DatabasePath = "Z:\\this\\does\\not\\exist.fasta";
+            var method = typeof(BioPolymerTabViewModel)
+                .GetMethod("LoadDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            Assert.DoesNotThrow(() => method.Invoke(vm, null));
+            Assert.That(vm.IsDatabaseLoaded, Is.False);
+        }
+
+        [Test]
+        public void LoadDatabase_NonExistentDatabase_DoesNotSetLoadedToTrue()
+        {
+            var logic = new DummyMetaDrawLogic();
+            logic.AllSpectralMatches = new List<SpectrumMatchFromTsv>
+            {
+                new DummySpectralmatch(accession: "ACC", baseSeq: "ABC"),
+                new DummySpectralmatch(accession: "ACC2", baseSeq: "DEF")
+            };
+            var vm = new BioPolymerTabViewModel(logic);
+
+            vm.DatabasePath = "C:\\db.fasta";
+            var method = typeof(BioPolymerTabViewModel)
+                .GetMethod("LoadDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            method.Invoke(vm, null);
+            Assert.That(vm.IsDatabaseLoaded, Is.False);
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(0));
+        }
+
+        [Test]
+        public void LoadDatabase_EmptyDatabase_DoesNotSetLoadedToTrue()
+        {
+            var logic = new DummyMetaDrawLogic();
+            logic.AllSpectralMatches = new List<SpectrumMatchFromTsv>
+            {
+                new DummySpectralmatch(accession: "ACC", baseSeq: "ABC"),
+                new DummySpectralmatch(accession: "ACC2", baseSeq: "DEF")
+            };
+            var vm = new BioPolymerTabViewModel(logic);
+
+            var dbPath = Path.Combine(Path.GetTempPath(), "empty.fasta");
+            File.WriteAllText(dbPath, string.Empty);
+
+            vm.DatabasePath = dbPath;
+            var method = typeof(BioPolymerTabViewModel)
+                .GetMethod("LoadDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            method.Invoke(vm, null);
+            Assert.That(vm.IsDatabaseLoaded, Is.False);
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(0));
+        }
+
+        [Test]
+        public void LoadDatabase_RealDatabase_LoadsWithoutIssue()
+        {
+            // Prepare Files
+            if (!EverythingRunnerEngineTestCase.TryGetTestCase(EverythingRunnerEngineTestCases.BottomUpQValue, out var searchTestCase))
+                Assert.Fail();
+
+            var dbPath = searchTestCase.DatabaseList.First().FilePath;
+            var smPath = Directory.GetFiles(searchTestCase.OutputDirectory, "*.psmtsv", SearchOption.AllDirectories).First();
+            var matches = SpectrumMatchTsvReader.ReadTsv(smPath, out _);
+
+            // Build View Model
+            var logic = new DummyMetaDrawLogic();
+            logic.AllSpectralMatches = matches;
+            var vm = new BioPolymerTabViewModel(logic);
+
+            // Test
+            vm.DatabasePath = dbPath;
+            var method = typeof(BioPolymerTabViewModel)
+                .GetMethod("LoadDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            method.Invoke(vm, null);
+            Thread.Sleep(1000); // wait for async load
+            Assert.That(vm.IsDatabaseLoaded, Is.True);
+        }
+
+        [Test]
+        public void ProcessSpectralMatches_HandlesSingleAccessionSingleLocalization()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            var allBioPolymersField = typeof(BioPolymerTabViewModel)
+                .GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            allBioPolymersField.SetValue(vm, new Dictionary<string, IBioPolymer>
+            {
+                { "ACC", new DummyBioPolymer("ACC", "Protein", "ABC") }
+            });
+            var match = new DummySpectralmatch(accession: "ACC", baseSeq: "ABC", missedCleavages: "0", startAndEnd: "[1 to 3]");
+            vm.ProcessSpectralMatches(new List<SpectrumMatchFromTsv> { match });
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(1));
+            var group = vm.AllGroups[0];
+            Assert.That(group.CoverageResults.Count, Is.EqualTo(1));
+            Assert.That(group.CoverageResults[0].CoverageType, Is.EqualTo(BioPolymerCoverageType.Unique));
+        }
+
+        [Test]
+        public void ProcessSpectralMatches_HandlesSingleAccessionSingleLocalization_MissedCleavage()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            var allBioPolymersField = typeof(BioPolymerTabViewModel)
+                .GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            allBioPolymersField.SetValue(vm, new Dictionary<string, IBioPolymer>
+            {
+                { "ACC", new DummyBioPolymer("ACC", "Protein", "ABC") }
+            });
+            var match = new DummySpectralmatch(accession: "ACC", baseSeq: "ABC", missedCleavages: "1", startAndEnd: "[1 to 3]");
+            vm.ProcessSpectralMatches(new List<SpectrumMatchFromTsv> { match });
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(1));
+            var group = vm.AllGroups[0];
+            Assert.That(group.CoverageResults[0].CoverageType, Is.EqualTo(BioPolymerCoverageType.UniqueMissedCleavage));
+        }
+
+        [Test]
+        public void ProcessSpectralMatches_HandlesMultipleAccessions()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            var allBioPolymersField = typeof(BioPolymerTabViewModel)
+                .GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            allBioPolymersField.SetValue(vm, new Dictionary<string, IBioPolymer>
+            {
+                { "ACC", new DummyBioPolymer("ACC", "Protein", "ABC") },
+                { "ACC2", new DummyBioPolymer("ACC2", "Protein2", "ABC") }
+            });
+            var match = new DummySpectralmatch(accession: "ACC|ACC2", baseSeq: "ABC", missedCleavages: "0|0", startAndEnd: "[1 to 3]|[1 to 3]");
+            vm.ProcessSpectralMatches(new List<SpectrumMatchFromTsv> { match });
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(2));
+            Assert.That(vm.AllGroups.All(g => g.CoverageResults[0].CoverageType == BioPolymerCoverageType.Shared));
+        }
+
+        [Test]
+        public void ProcessSpectralMatches_HandlesSingleAccessionMultipleLocalizations()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            var allBioPolymersField = typeof(BioPolymerTabViewModel)
+                .GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            allBioPolymersField.SetValue(vm, new Dictionary<string, IBioPolymer>
+            {
+                { "ACC", new DummyBioPolymer("ACC", "Protein", "ABC") }
+            });
+            var match = new DummySpectralmatch(accession: "ACC", baseSeq: "ABC", missedCleavages: "0", startAndEnd: "[1 to 2]|[2 to 3]");
+            vm.ProcessSpectralMatches(new List<SpectrumMatchFromTsv> { match });
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(1));
+            var group = vm.AllGroups[0];
+            Assert.That(group.CoverageResults.Count, Is.EqualTo(2));
+            Assert.That(group.CoverageResults.All(r => r.CoverageType == BioPolymerCoverageType.TandemRepeat));
+        }
+
+        [Test]
+        public void ProcessSpectralMatches_HandlesMultipleAccessionsSingleLocalization()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            var allBioPolymersField = typeof(BioPolymerTabViewModel)
+                .GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            allBioPolymersField.SetValue(vm, new Dictionary<string, IBioPolymer>
+            {
+                { "ACC", new DummyBioPolymer("ACC", "Protein", "ABC") },
+                { "ACC2", new DummyBioPolymer("ACC2", "Protein2", "ABC") }
+            });
+            var match = new DummySpectralmatch(accession: "ACC|ACC2", baseSeq: "ABC", missedCleavages: "0|0", startAndEnd: "[1 to 3]");
+            vm.ProcessSpectralMatches(new List<SpectrumMatchFromTsv> { match });
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(2));
+            Assert.That(vm.AllGroups.All(g => g.CoverageResults[0].CoverageType == BioPolymerCoverageType.Shared));
+        }
+
+        [Test]
+        public void ProcessSpectralMatches_HandlesMissedCleavageTandemRepeats()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            var allBioPolymersField = typeof(BioPolymerTabViewModel)
+                .GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            allBioPolymersField.SetValue(vm, new Dictionary<string, IBioPolymer>
+            {
+                { "ACC", new DummyBioPolymer("ACC", "Protein", "ABCDABC") },
+            });
+            var match = new DummySpectralmatch(accession: "ACC", baseSeq: "ABC", missedCleavages: "1", startAndEnd: "[1 to 3]|[5 to 7]");
+            vm.ProcessSpectralMatches(new List<SpectrumMatchFromTsv> { match });
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(1));
+            Assert.That(vm.AllGroups.All(g => g.CoverageResults[0].CoverageType == BioPolymerCoverageType.TandemRepeatMissedCleavage));
+        }
+
+        [Test]
+        public void ExportImage_DoesNothing_IfCoverageDrawingIsNull()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+            vm.CoverageMapViewModel.CoverageDrawing = null;
+            var method = typeof(BioPolymerTabViewModel)
+                .GetMethod("ExportImage", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            Assert.DoesNotThrow(() => method.Invoke(vm, null));
+        }
+
+        [Test]
+        public void ExportImage_ExportsImage_WhenCoverageDrawingIsPresent()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic, Path.GetTempPath());
+            // Setup a dummy DrawingImage
+            var drawingVisual = new DrawingVisual();
+            using (var dc = drawingVisual.RenderOpen())
+            {
+                dc.DrawRectangle(Brushes.Red, null, new System.Windows.Rect(0, 0, 100, 100));
+            }
+            var drawingImage = new DrawingImage(drawingVisual.Drawing);
+            vm.CoverageMapViewModel.CoverageDrawing = drawingImage;
+            // Setup a selected group for export path
+            vm.SelectedGroup = new BioPolymerGroupViewModel("ACC", "Protein", "ABC", new List<BioPolymerCoverageResultModel>());
+            var method = typeof(BioPolymerTabViewModel)
+                .GetMethod("ExportImage", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+            MessageBoxHelper.SuppressMessageBoxes = true;
+            Assert.DoesNotThrow(() => method.Invoke(vm, null));
+            // Check that file was created
+            var expectedPath = Path.Combine(vm.ExportDirectory, "ACC_SequenceCoverage.Pdf");
+            Assert.That(File.Exists(expectedPath), Is.True);
+            File.Delete(expectedPath);
+        }
+
+        [Test]
+        public void ResetDatabase_ClearsAllBioPolymers()
+        {
+            // Prepare Files
+            if (!EverythingRunnerEngineTestCase.TryGetTestCase(EverythingRunnerEngineTestCases.BottomUpQValue, out var searchTestCase))
+                Assert.Fail();
+
+            var dbPath = searchTestCase.DatabaseList.First().FilePath;
+            var smPath = Directory.GetFiles(searchTestCase.OutputDirectory, "*.psmtsv", SearchOption.AllDirectories).First();
+            var matches = Readers.SpectrumMatchTsvReader.ReadTsv(smPath, out _);
+
+            // Build View Model
+            var logic = new DummyMetaDrawLogic();
+            logic.AllSpectralMatches = matches;
+            var vm = new BioPolymerTabViewModel(logic);
+
+            vm.DatabasePath = dbPath;
+            var method = typeof(BioPolymerTabViewModel)
+                .GetMethod("LoadDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)!
+                .Invoke(vm, null);
+
+            var allBioPolymersField = typeof(BioPolymerTabViewModel)
+                .GetField("_allBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
+
+            // Call ResetDatabase
+            vm.GetType().GetMethod("ResetDatabase", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)!
+                .Invoke(vm, null);
+
+            // Assert all cleared
+            Assert.That(vm.DatabasePath, Is.Empty);
+            Assert.That(vm.DatabaseName, Is.Empty);
+            Assert.That(vm.AllGroups.Count, Is.EqualTo(0));
+            Assert.That(vm.FilteredGroups.Count, Is.EqualTo(0));
+            var clearedDict = allBioPolymersField.GetValue(vm) as Dictionary<string, IBioPolymer>;
+            Assert.That(clearedDict, Is.Not.Null);
+            Assert.That(clearedDict.Count, Is.EqualTo(0));
+        }
+
+        [Test]
+        public void SelectedGroup_Setter_UpdatesGroupAndCoverageDrawing()
+        {
+            var logic = new DummyMetaDrawLogic();
+            var vm = new BioPolymerTabViewModel(logic);
+
+            // Create two groups with different sequences
+            var group1 = new BioPolymerGroupViewModel("A1", "Alpha", "ABC", new[] {
+                new BioPolymerCoverageResultModel(new DummySpectralmatch(), "ABC", 1, 3, BioPolymerCoverageType.Unique)
+            });
+            var group2 = new BioPolymerGroupViewModel("B2", "Beta", "DEF", new[] {
+                new BioPolymerCoverageResultModel(new DummySpectralmatch(), "DEF", 1, 3, BioPolymerCoverageType.Shared)
+            });
+
+            // Set first group and capture the plot
+            vm.SelectedGroup = group1;
+            var firstDrawing = vm.CoverageMapViewModel.CoverageDrawing;
+
+            // Set second group and capture the plot
+            vm.SelectedGroup = group2;
+            var secondDrawing = vm.CoverageMapViewModel.CoverageDrawing;
+
+            // Assert that the selected group and CoverageMapViewModel.Group are updated
+            Assert.That(vm.SelectedGroup, Is.EqualTo(group2));
+            Assert.That(vm.CoverageMapViewModel.Group, Is.EqualTo(group2));
+
+            // Assert that the plot changes when the group changes
+            Assert.That(firstDrawing, Is.Not.Null);
+            Assert.That(secondDrawing, Is.Not.Null);
+            Assert.That(secondDrawing, Is.Not.EqualTo(firstDrawing));
+        }
+
+    }
+}
diff --git a/MetaMorpheus/Test/MetaDraw/ChimeraAnalysisTabViewModelTests.cs b/MetaMorpheus/Test/MetaDraw/ChimeraAnalysisTabViewModelTests.cs
index 404f88059..8a17ee946 100644
--- a/MetaMorpheus/Test/MetaDraw/ChimeraAnalysisTabViewModelTests.cs
+++ b/MetaMorpheus/Test/MetaDraw/ChimeraAnalysisTabViewModelTests.cs
@@ -59,7 +59,8 @@ public void ChimeraTabViewModel_ResultsFilteredCorrectly()
             {"FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile }
         };
 
-        var chimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel(ChimeraGroupViewModelTests.AllMatches, dataFiles, TestExportDirectory);
+        var chimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel(TestExportDirectory);
+        chimeraAnalysisTabViewModel.ProcessChimeraData(ChimeraGroupViewModelTests.AllMatches, dataFiles);
         Assert.That(chimeraAnalysisTabViewModel.ChimeraGroupViewModels.All(p => p.Count > 1),
             Is.True, "All chimera groups should have at least two PSMs.");
         Assert.That(chimeraAnalysisTabViewModel.ChimeraGroupViewModels.Count, Is.GreaterThan(0), "There should be at least one chimera group.");
@@ -76,7 +77,8 @@ public void ChimeraTabViewModel_ResultsFilteredCorrectly()
         MetaDrawSettings.QValueFilter = 0.5; // set filter higher
         MetaDrawSettings.ShowDecoys = true; // show decoys
 
-        chimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel(ChimeraGroupViewModelTests.AllMatches, dataFiles, TestExportDirectory);
+        chimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel(TestExportDirectory);
+        chimeraAnalysisTabViewModel.ProcessChimeraData(ChimeraGroupViewModelTests.AllMatches, dataFiles);
         Assert.That(chimeraAnalysisTabViewModel.ChimeraGroupViewModels.All(p => p.Count > 1),
             Is.True, "All chimera groups should have at least two PSMs after changing settings.");
         Assert.That(chimeraAnalysisTabViewModel.ChimeraGroupViewModels.Count, Is.GreaterThan(0), "There should still be at least one chimera group after changing settings.");
@@ -97,13 +99,15 @@ public void ChimeraTabViewModel_ResultsFilteredCorrectly()
     }
 
     [Test]
+    [NonParallelizable]
     public static void ChimeraTabViewModel_PrecursorAssignmentIsCorrectInGroups()
     {
         var dataFiles = new Dictionary<string, MsDataFile>()
         {
             {"FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile }
         };
-        var chimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel(ChimeraGroupViewModelTests.AllMatches, dataFiles, TestExportDirectory);
+        var chimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel(TestExportDirectory);
+        chimeraAnalysisTabViewModel.ProcessChimeraData(ChimeraGroupViewModelTests.AllMatches, dataFiles);
 
         foreach (var chimeraGroup in chimeraAnalysisTabViewModel.ChimeraGroupViewModels)
         {
@@ -122,7 +126,11 @@ public static void ChimeraTabViewModel_PrecursorAssignmentIsCorrectInGroups()
                 for (int j = 0; j < chimericPsms.Count; j++)
                 {
                     if (i == j) continue;
+
                     var otherEnvelope = chimericPsms[j].PrecursorEnvelope;
+                    if (psm.ChargeState != otherEnvelope.Charge) 
+                        continue;
+
                     double diff = Math.Abs(psm.PrecursorMass - otherEnvelope.MonoisotopicMass);
                     Assert.That(minDiff, Is.LessThanOrEqualTo(diff),
                         $"PSM {i} in group (scan {chimeraGroup.Ms2ScanNumber}) should be assigned to its closest envelope.");
@@ -140,7 +148,8 @@ public void Constructor_InitializesProperties()
         string exportDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests");
 
         // Act
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles, exportDir);
+        var vm = new ChimeraAnalysisTabViewModel(exportDir);
+        vm.ProcessChimeraData(allPsms, dataFiles);
 
         // Assert
         Assert.That(vm.ChimeraGroupViewModels, Is.Not.Null.And.Not.Empty);
@@ -157,7 +166,8 @@ public void ChimeraDrawnSequence_Setter_Notifies()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         var group = vm.ChimeraGroupViewModels[0];
         var canvas = new Canvas();
         var drawnSeq = new ChimeraDrawnSequence(canvas, group);
@@ -178,7 +188,8 @@ public void UseLetterOnly_Setter_UpdatesIonColorsAndNotifies()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         bool propertyChanged = false;
         vm.PropertyChanged += (s, e) => { if (e.PropertyName == nameof(vm.UseLetterOnly)) propertyChanged = true; };
 
@@ -198,7 +209,8 @@ public void ExportDirectory_Setter_CreatesDirectoryAndNotifies()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         string tempDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests_ExportDir");
         if (Directory.Exists(tempDir))
             Directory.Delete(tempDir, true);
@@ -223,7 +235,8 @@ public void ExportMs1Command_DoesNothing_WhenSelectedChimeraGroupIsNull()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
 
         string tempDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests_ExportMs1_Null");
         vm.ExportDirectory = tempDir;
@@ -243,7 +256,8 @@ public void ExportMs2Command_DoesNothing_WhenSelectedChimeraGroupIsNull()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
 
         string tempDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests_ExportMs2_Null");
         vm.ExportDirectory = tempDir;
@@ -263,7 +277,8 @@ public void ExportLegendCommand_DoesNothing_WhenArgumentIsNull()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         string tempDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests_ExportLegend_Null");
         vm.ExportDirectory = tempDir;
         Directory.CreateDirectory(tempDir);
@@ -282,7 +297,8 @@ public void ExportMs1Command_ExportsCorrectFormat()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         vm.SelectedChimeraGroup = vm.ChimeraGroupViewModels[0];
         string tempDir = Path.Combine(Path.GetTempPath(), $"ChimeraAnalysisTabViewModelTests_ExportMs1_{MetaDrawSettings.ExportType}");
         vm.ExportDirectory = tempDir;
@@ -314,7 +330,8 @@ public void ExportMs2Command_ExportsCorrectFormat()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         vm.SelectedChimeraGroup = vm.ChimeraGroupViewModels[0];
         string tempDir = Path.Combine(Path.GetTempPath(), $"ChimeraAnalysisTabViewModelTests_ExportMs2_{MetaDrawSettings.ExportType}");
         vm.ExportDirectory = tempDir;
@@ -346,7 +363,8 @@ public void ExportSequenceCoverageCommand_InvokesExportSequenceCoverage()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         vm.SelectedChimeraGroup = vm.ChimeraGroupViewModels[0];
         string tempDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests_ExportSeqCov");
         vm.ExportDirectory = tempDir;
@@ -386,7 +404,8 @@ public void ExportLegendCommand_InvokesExportLegend()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         vm.SelectedChimeraGroup = vm.ChimeraGroupViewModels[0];
         string tempDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests_ExportLegend");
         vm.ExportDirectory = tempDir;
@@ -441,7 +460,8 @@ public void PrecursorIonAnnotations_AreLetterOnly_WhenUseLetterOnlyIsTrue()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
 
         // Act
         vm.UseLetterOnly = true;
@@ -470,7 +490,8 @@ public void ChimeraSpectrumMatchPlot_GetterSetter_Works()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         var plotView = new OxyPlot.Wpf.PlotView();
         var group = vm.ChimeraGroupViewModels[0];
         var plot = new ChimeraSpectrumMatchPlot(plotView, group);
@@ -488,7 +509,8 @@ public void Ms1ChimeraPlot_GetterSetter_Works()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         var plotView = new OxyPlot.Wpf.PlotView();
         var group = vm.ChimeraGroupViewModels[0];
         var plot = new Ms1ChimeraPlot(plotView, group);
@@ -506,7 +528,8 @@ public void ExportMs2Command_ExportsWithLegend_AndLegendWithinBounds()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         vm.SelectedChimeraGroup = vm.ChimeraGroupViewModels[0];
         string tempDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests_ExportMs2_Legend");
         vm.ExportDirectory = tempDir;
@@ -557,7 +580,8 @@ public void ExportAllCommand_ExportsWithLegend_AndLegendWithinBounds()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         vm.SelectedChimeraGroup = vm.ChimeraGroupViewModels[0];
         string tempDir = Path.Combine(Path.GetTempPath(), "ChimeraAnalysisTabViewModelTests_ExportAll_Legend");
         vm.ExportDirectory = tempDir;
@@ -617,7 +641,8 @@ public void CombinePlotAndLegend_CombinesBitmaps_WhenLegendPresent()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
 
         var plotView = new Canvas { Width = 200, Height = 100, Background = System.Windows.Media.Brushes.White };
         var legend = new Canvas { Width = 50, Height = 30, Background = System.Windows.Media.Brushes.White };
@@ -672,7 +697,8 @@ public void CombinePlotAndLegend_ReturnsPlotBitmap_WhenLegendIsNull()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
 
         var plotView = new Canvas { Width = 200, Height = 100, Background = System.Windows.Media.Brushes.White };
 
diff --git a/MetaMorpheus/Test/MetaDraw/ChimeraGroupViewModelTests.cs b/MetaMorpheus/Test/MetaDraw/ChimeraGroupViewModelTests.cs
index 7fccff87b..33632c139 100644
--- a/MetaMorpheus/Test/MetaDraw/ChimeraGroupViewModelTests.cs
+++ b/MetaMorpheus/Test/MetaDraw/ChimeraGroupViewModelTests.cs
@@ -293,7 +293,8 @@ public void ChimeraGroupViewModel_AssignIonColors_UsesLetterOption()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         var group = vm.ChimeraGroupViewModels[0];
 
         // Act
@@ -321,7 +322,8 @@ public void AssignIonColors_ProduceExpectedAnnotations()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles);
+        var vm = new ChimeraAnalysisTabViewModel();
+        vm.ProcessChimeraData(allPsms, dataFiles);
         var group = vm.ChimeraGroupViewModels[0];
 
         // Act
@@ -350,11 +352,13 @@ public void AssignIonColors_ProduceLetterOnlyAnnotations()
         // Arrange
         var allPsms = ChimeraGroupViewModelTests.AllMatches;
         var dataFiles = new Dictionary<string, MsDataFile> { { "FXN3_tr1_032017-calib", ChimeraGroupViewModelTests.DataFile } };
-        var vm = new ChimeraAnalysisTabViewModel(allPsms, dataFiles)
+
+        var vm = new ChimeraAnalysisTabViewModel()
         {
             UseLetterOnly = true
         };
-        vm.UseLetterOnly = true;
+        vm.ProcessChimeraData(allPsms, dataFiles);
+
         var group = vm.ChimeraGroupViewModels[0];
 
         // Act
diff --git a/MetaMorpheus/Test/MetaDraw/DeconExplorationTabViewModelTests.cs b/MetaMorpheus/Test/MetaDraw/DeconExplorationTabViewModelTests.cs
new file mode 100644
index 000000000..2a2c4d9ae
--- /dev/null
+++ b/MetaMorpheus/Test/MetaDraw/DeconExplorationTabViewModelTests.cs
@@ -0,0 +1,225 @@
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.IO;
+using System.Linq;
+using System.Threading;
+using EngineLayer;
+using GuiFunctions;
+using GuiFunctions.MetaDraw;
+using MassSpectrometry;
+using NUnit.Framework;
+using OxyPlot.Wpf;
+using Readers;
+
+namespace Test.MetaDraw;
+
+[TestFixture]
+public class DeconExplorationTabViewModelTests
+{
+    private string mzmlPath;
+    private MsDataFile msDataFile;
+    private MetaDrawLogic metaDrawLogic;
+    private MetaDrawLogic realDataLoaded;
+    private List<SpectrumMatchFromTsv> realPsms;
+
+    [OneTimeSetUp]
+    public void Setup()
+    {
+        // Path to the test mzML file
+        mzmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "SmallCalibratible_Yeast.mzML");
+        Assert.That(File.Exists(mzmlPath), $"Test mzML file not found: {mzmlPath}");
+        msDataFile = MsDataFileReader.GetDataFile(mzmlPath).LoadAllStaticData();
+        metaDrawLogic = new MetaDrawLogic();
+
+        var key = System.IO.Path.GetFileName(mzmlPath.Replace(GlobalVariables.GetFileExtension(mzmlPath), string.Empty));
+        metaDrawLogic.MsDataFiles.Add(key, msDataFile);
+
+        // Set up real data tests
+        realDataLoaded = new();
+        var psmPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "TopDownTestData", "TDGPTMDSearchResults.psmtsv");
+        string msDataPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "TopDownTestData", "TDGPTMDSearchSingleSpectra.mzML");
+        key = System.IO.Path.GetFileName(msDataPath.Replace(GlobalVariables.GetFileExtension(msDataPath), string.Empty));
+        realDataLoaded.SpectraFilePaths.Add(msDataPath);
+        realDataLoaded.SpectralMatchResultFilePaths.Add(psmPath);   
+        new MetaDrawDataLoader(realDataLoaded).LoadAllAsync(true, true, true).Wait();
+
+        var file = realDataLoaded.MsDataFiles.First().Value;
+        realDataLoaded.MsDataFiles.Clear();
+        realDataLoaded.MsDataFiles.Add("SmallCalibratible_Yeast", file);
+        realPsms = realDataLoaded.AllSpectralMatches;
+    }
+
+    [Test]
+    public void PopulateScansCollection_FullSpectrumMode_AddsAllScans()
+    {
+        var vm = new DeconExplorationTabViewModel(metaDrawLogic);
+        vm.Mode = DeconvolutionMode.FullSpectrum;
+        vm.SelectedMsDataFile = msDataFile;
+
+        Thread.Sleep(3000); // wait for async load
+        Assert.That(vm.Scans.Count, Is.EqualTo(msDataFile.GetMsDataScans().Count()));
+    }
+
+    [Test]
+    public void PopulateScansCollection_IsolationRegionMode_AddsOnlyMs2()
+    {
+        var vm = new DeconExplorationTabViewModel(metaDrawLogic);
+        vm.Mode = DeconvolutionMode.IsolationRegion;
+        vm.SelectedMsDataFile = msDataFile;
+
+        Assert.That(vm.Scans.All(s => s.MsnOrder == 2));
+    }
+
+    [Test]
+    public void Changing_Mode_RefreshesScans()
+    {
+        var vm = new DeconExplorationTabViewModel(metaDrawLogic);
+        vm.SelectedMsDataFile = msDataFile;
+        vm.Mode = DeconvolutionMode.FullSpectrum;
+        Thread.Sleep(1000); // wait for async load
+
+        int allCount = vm.Scans.Count;
+        vm.Mode = DeconvolutionMode.IsolationRegion;
+        Thread.Sleep(1000); // wait for async load
+        int ms2Count = vm.Scans.Count;
+
+        Assert.That(allCount, Is.GreaterThan(ms2Count));
+        Assert.That(vm.Scans.All(s => s.MsnOrder == 2));
+    }
+
+    [Test]
+    public void RunDeconvolutionCommand_DoesNotThrow_WhenNoScanSelected()
+    {
+        var vm = new DeconExplorationTabViewModel(metaDrawLogic);
+        Assert.DoesNotThrow(() => vm.RunDeconvolutionCommand.Execute(null));
+    }
+
+    [Test, Apartment(System.Threading.ApartmentState.STA)]
+    public void RunDeconvolutionCommand_FullSpectrumMode_PopulatesDeconvolutedSpecies()
+    {
+        var vm = new DeconExplorationTabViewModel(metaDrawLogic);
+        vm.Mode = DeconvolutionMode.FullSpectrum;
+        vm.SelectedMsDataFile = msDataFile;
+        vm.SelectedMsDataScan = msDataFile.GetMsDataScans().FirstOrDefault();
+        vm.RunDeconvolutionCommand.Execute(new PlotView());
+
+        Assert.That(vm.DeconvolutedSpecies.Count, Is.GreaterThanOrEqualTo(0));
+    }
+
+    [Test, Apartment(System.Threading.ApartmentState.STA)]
+    public void RunDeconvolutionCommand_IsolationRegionMode_PopulatesDeconvolutedSpecies()
+    {
+        var vm = new DeconExplorationTabViewModel(metaDrawLogic);
+        Assert.That(vm.IsLoading, Is.False);
+        vm.Mode = DeconvolutionMode.IsolationRegion;
+        vm.SelectedMsDataFile = msDataFile;
+        var ms2 = msDataFile.GetMsDataScans().FirstOrDefault(s => s.MsnOrder == 2);
+        if (ms2 == null)
+            Assert.Inconclusive("No MS2 scan in test file.");
+        vm.SelectedMsDataScan = ms2;
+        vm.RunDeconvolutionCommand.Execute(new PlotView());
+
+        Assert.That(vm.DeconvolutedSpecies.Count, Is.GreaterThanOrEqualTo(0));
+    }
+
+    [Test, Apartment(System.Threading.ApartmentState.STA)]
+    public void RunDeconvolutionCommand_FullSpectrumMode_LimitsAxis()
+    {
+        var vm = new DeconExplorationTabViewModel(metaDrawLogic);
+        vm.Mode = DeconvolutionMode.FullSpectrum;
+        vm.SelectedMsDataFile = msDataFile;
+        vm.SelectedMsDataScan = msDataFile.GetMsDataScans().FirstOrDefault();
+        vm.RunDeconvolutionCommand.Execute(new PlotView());
+
+        var specRange = vm.SelectedMsDataScan!.MassSpectrum.Range;
+        var xAxis = vm.Plot!.Model.Axes[0];
+        Assert.That(xAxis.Minimum, Is.EqualTo(specRange.Minimum).Within(5));
+        Assert.That(xAxis.Maximum, Is.EqualTo(specRange.Maximum).Within(5));
+
+        Assert.That(vm.MinMzToPlot, Is.EqualTo(0));
+        vm.MinMzToPlot = 800;
+        vm.RunDeconvolutionCommand.Execute(new PlotView());
+        xAxis = vm.Plot!.Model.Axes[0];
+        Assert.That(xAxis.ActualMinimum, Is.EqualTo(800).Within(5));
+        Assert.That(xAxis.ActualMaximum, Is.EqualTo(specRange.Maximum).Within(5));
+
+        Assert.That(vm.MaxMzToPlot, Is.EqualTo(0));
+        vm.MaxMzToPlot = 1200;
+        vm.RunDeconvolutionCommand.Execute(new PlotView());
+        xAxis = vm.Plot!.Model.Axes[0];
+        Assert.That(xAxis.ActualMinimum, Is.EqualTo(800).Within(5));
+        Assert.That(xAxis.ActualMaximum, Is.EqualTo(1200).Within(5));
+    }
+
+    [Test]
+    public void DeconvolutionModes_ContainsAllModes()
+    {
+        var vm = new DeconExplorationTabViewModel(metaDrawLogic);
+        var modes = vm.DeconvolutionModes;
+        Assert.That(modes, Does.Contain(DeconvolutionMode.FullSpectrum));
+        Assert.That(modes, Does.Contain(DeconvolutionMode.IsolationRegion));
+    }
+
+    [Test, Apartment(ApartmentState.STA)]
+    public void DeconPlot_AnnotatePlot_ReturnsEarlyOnNullOrEmpty()
+    {
+        var plotView = new PlotView();
+        var scan = msDataFile.LoadAllStaticData().GetMsDataScans().First();
+        var deconResults = new List<DeconvolutedSpeciesViewModel>();
+        var plot = new DeconvolutionPlot(plotView, scan, deconResults, DeconvolutionMode.FullSpectrum);
+
+        Assert.DoesNotThrow(() => plot.AnnotatePlot(null!));
+        Assert.DoesNotThrow(() => plot.AnnotatePlot(new List<DeconvolutedSpeciesViewModel>()));
+    }
+
+    [Test]
+    public void OnlyIdentifiedScans_FiltersScans_FullSpectrumMode()
+    {
+        var vm = new DeconExplorationTabViewModel(realDataLoaded);
+        vm.MsDataFiles.Add(realDataLoaded.MsDataFiles.Values.First());
+        vm.SelectedMsDataFile = vm.MsDataFiles.First();
+        vm.Mode = DeconvolutionMode.FullSpectrum;
+        Thread.Sleep(1000); // wait for async load
+
+        // Simulate identified scans
+        var scanCount = vm.Scans.Count;
+
+        var acceptableScanNumbers = realPsms.Select(p => p.Ms2ScanNumber)
+            .Concat(realPsms.Select(p => p.PrecursorScanNum)).ToHashSet();
+
+        vm.OnlyIdentifiedScans = true;
+        Thread.Sleep(1000); // wait for async load
+        var scanCountAfterFilter = vm.Scans.Count;
+        Assert.That(scanCountAfterFilter, Is.LessThan(scanCount));
+        var expectedScanNumbers = acceptableScanNumbers.Intersect(vm.Scans.Select(s => s.OneBasedScanNumber)).ToHashSet();
+        var actualScanNumbers = vm.Scans.Select(s => s.OneBasedScanNumber).ToHashSet();
+
+        Assert.That(actualScanNumbers, Is.EquivalentTo(expectedScanNumbers));
+    }
+
+    [Test]
+    public void OnlyIdentifiedScans_FiltersScans_IsolationRegionMode()
+    {
+        var vm = new DeconExplorationTabViewModel(realDataLoaded);
+        vm.MsDataFiles.Add(realDataLoaded.MsDataFiles.Values.First());
+        vm.SelectedMsDataFile = vm.MsDataFiles.First();
+        vm.Mode = DeconvolutionMode.IsolationRegion;
+        Thread.Sleep(1000); // wait for async load
+
+        // Simulate identified scans
+        var scanCount = vm.Scans.Count;
+
+        var acceptableScanNumbers = realPsms.Select(p => p.Ms2ScanNumber)
+            .ToHashSet();
+
+        vm.OnlyIdentifiedScans = true;
+        Thread.Sleep(1000); // wait for async load
+        var scanCountAfterFilter = vm.Scans.Count;
+        Assert.That(scanCountAfterFilter, Is.LessThan(scanCount));
+        var expectedScanNumbers = acceptableScanNumbers.Intersect(vm.Scans.Select(s => s.OneBasedScanNumber)).ToHashSet();
+        var actualScanNumbers = vm.Scans.Select(s => s.OneBasedScanNumber).ToHashSet();
+
+        Assert.That(actualScanNumbers, Is.EquivalentTo(expectedScanNumbers));
+        Assert.That(vm.Scans.All(s => s.MsnOrder == 2));
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/Test/MetaDraw/DeconvolutedSpeciesViewModelTests.cs b/MetaMorpheus/Test/MetaDraw/DeconvolutedSpeciesViewModelTests.cs
new file mode 100644
index 000000000..758f04455
--- /dev/null
+++ b/MetaMorpheus/Test/MetaDraw/DeconvolutedSpeciesViewModelTests.cs
@@ -0,0 +1,71 @@
+using System.Collections.Generic;
+using System.Linq;
+using Chemistry;
+using GuiFunctions;
+using MassSpectrometry;
+using NUnit.Framework;
+using OxyPlot;
+
+namespace Test.MetaDraw;
+
+[TestFixture]
+public class DeconvolutedSpeciesViewModelTests
+{
+    [Test]
+    public void Properties_AreCorrect()
+    {
+        // Arrange: create a fake isotopic envelope
+        var peaks = new List<(double mz, double intensity)>
+        {
+            (500.0, 100.0),
+            (501.0, 200.0),
+            (502.0, 50.0)
+        };
+        var envelope = new IsotopicEnvelope(0, peaks, 1000, 2, peaks.Sum(p => p.intensity), 1);
+
+        // Act
+        var vm = new DeconvolutedSpeciesViewModel(envelope);
+
+        // Assert
+        Assert.That(vm.Envelope, Is.EqualTo(envelope));
+        Assert.That(vm.Color, Is.EqualTo(OxyColors.Automatic));
+        Assert.That(vm.MonoisotopicMass, Is.EqualTo(1000.0));
+        Assert.That(vm.Charge, Is.EqualTo(2));
+        Assert.That(vm.PeakCount, Is.EqualTo(3));
+        Assert.That(vm.Intensity, Is.EqualTo(350.0));
+        Assert.That(vm.Annotation, Does.Contain("M=1000"));
+        Assert.That(vm.Annotation, Does.Contain("z=2"));
+        Assert.That(vm.MostAbundantMz, Is.EqualTo(501.0));
+        Assert.That(vm.PeakMzs, Is.EqualTo("500, 501, 502"));
+        Assert.That(vm.MonoMz, Is.EqualTo(1000.0.ToMz(2)));
+
+    }
+
+    [Test]
+    public void Properties_CacheValues()
+    {
+        // Arrange
+        var peaks = new List<(double mz, double intensity)>
+        {
+            (100, 1), (200, 2)
+        };
+        var envelope = new IsotopicEnvelope(0, peaks, 1000, 3, peaks.Sum(p => p.intensity), 1);
+        var vm = new DeconvolutedSpeciesViewModel(envelope);
+
+        // Act
+        var intensity1 = vm.Intensity;
+        var intensity2 = vm.Intensity;
+        var annotation1 = vm.Annotation;
+        var annotation2 = vm.Annotation;
+        var mostAbundantMz1 = vm.MostAbundantMz;
+        var mostAbundantMz2 = vm.MostAbundantMz;
+        var peakMzs1 = vm.PeakMzs;
+        var peakMzs2 = vm.PeakMzs;
+
+        // Assert: values are cached and consistent
+        Assert.That(intensity1, Is.EqualTo(intensity2));
+        Assert.That(annotation1, Is.EqualTo(annotation2));
+        Assert.That(mostAbundantMz1, Is.EqualTo(mostAbundantMz2));
+        Assert.That(peakMzs1, Is.EqualTo(peakMzs2));
+    }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawDataLoaderTests.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawDataLoaderTests.cs
new file mode 100644
index 000000000..8627f030d
--- /dev/null
+++ b/MetaMorpheus/Test/MetaDraw/MetaDrawDataLoaderTests.cs
@@ -0,0 +1,246 @@
+using System.IO;
+using System.Linq;
+using System.Threading;
+using System.Threading.Tasks;
+using GuiFunctions.MetaDraw;
+using NUnit.Framework;
+using Readers;
+using GuiFunctions;
+using MassSpectrometry;
+
+namespace Test.MetaDraw;
+
+[TestFixture]
+public class MetaDrawDataLoaderTests
+{
+    private string mzmlPath;
+    private MsDataFile msDataFile;
+    private MetaDrawLogic logic;
+    private MetaDrawDataLoader loader;
+
+    [OneTimeSetUp]
+    public void OneTimeSetup()
+    {
+        mzmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "SmallCalibratible_Yeast.mzML");
+
+        Assert.That(File.Exists(mzmlPath), $"Test mzML file not found: {mzmlPath}");
+        msDataFile = MsDataFileReader.GetDataFile(mzmlPath).LoadAllStaticData();
+
+        logic = new MetaDrawLogic();
+        loader = new MetaDrawDataLoader(logic);
+    }
+
+    [SetUp]
+    public void SetUp()
+    {
+        logic.CleanUpResources();
+    }
+
+    [Test]
+    public async Task LoadSpectraAsync_LoadsSpectraFiles()
+    {
+        logic.SpectraFilePaths.Add(mzmlPath);
+        var errors = await loader.LoadSpectraAsync(CancellationToken.None);
+        Assert.That(errors, Is.Empty);
+        Assert.That(logic.MsDataFiles.Count, Is.EqualTo(1));
+        Assert.That(logic.MsDataFiles.Values.First().GetMsDataScans().Count(), Is.GreaterThan(0));
+    }
+
+    [Test]
+    public async Task LoadSpectraAsync_Cancellation_Throws()
+    {
+        var cts = new CancellationTokenSource();
+        cts.Cancel();
+        Assert.ThrowsAsync<TaskCanceledException>(async () => await loader.LoadSpectraAsync(cts.Token));
+    }
+
+    [Test]
+    public async Task LoadPsmsAsync_NoFiles_ReturnsEmpty()
+    {
+        var errors = await loader.LoadPsmsAsync(false, CancellationToken.None);
+        Assert.That(errors, Is.Empty);
+    }
+
+    [Test]
+    public async Task LoadLibrariesAsync_NoFiles_ReturnsEmpty()
+    {
+        var errors = await loader.LoadLibrariesAsync(CancellationToken.None);
+        Assert.That(errors, Is.Empty);
+    }
+
+    [Test]
+    public async Task LoadAllAsync_SpectraOnly_LoadsSpectra()
+    {
+        logic.SpectraFilePaths.Add(mzmlPath);
+        var errors = await loader.LoadAllAsync(true, false, false);
+        Assert.That(errors, Is.Empty);
+        Assert.That(logic.MsDataFiles.Count, Is.EqualTo(1));
+    }
+
+    [Test]
+    public void ProcessBioPolymerTab_EnablesTabAndSetsExportDirectory()
+    {
+        var bioPolymerTab = new BioPolymerTabViewModel(logic, "C:\\Export");
+        logic.AllSpectralMatches.Add(new DummySpectralmatch());
+        loader.GetType().GetMethod("ProcessBioPolymerTab", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { bioPolymerTab, "C:\\Export", CancellationToken.None });
+        Assert.That(bioPolymerTab.IsTabEnabled, Is.True);
+        Assert.That(bioPolymerTab.ExportDirectory, Is.EqualTo("C:\\Export"));
+    }
+
+    [Test]
+    public void ProcessBioPolymerTab_LoadsDatabase()
+    {
+        var bioPolymerTab = new BioPolymerTabViewModel(logic, "C:\\Export");
+        bioPolymerTab.DatabasePath = Path.Combine(TestContext.CurrentContext.TestDirectory,
+            @"TestData\TaGe_SA_A549_3_snip.fasta");
+        logic.AllSpectralMatches.Add(new DummySpectralmatch());
+        loader.GetType().GetMethod("ProcessBioPolymerTab", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { bioPolymerTab, "C:\\Export", CancellationToken.None });
+        Assert.That(bioPolymerTab.IsTabEnabled, Is.True);
+        Assert.That(bioPolymerTab.ExportDirectory, Is.EqualTo("C:\\Export"));
+    }
+
+    [Test]
+    public void ProcessDeconTab_EnablesTabAndSetsExportDirectory()
+    {
+        var deconTab = new DeconExplorationTabViewModel(logic);
+        logic.MsDataFiles.Clear();
+        logic.MsDataFiles.Add("test", msDataFile);
+        loader.GetType().GetMethod("ProcessDeconTab", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { deconTab, "C:\\Export", CancellationToken.None });
+        Assert.That(deconTab.IsTabEnabled, Is.True);
+        Assert.That(deconTab.ExportDirectory, Is.EqualTo("C:\\Export"));
+        Assert.That(deconTab.MsDataFiles.Count, Is.EqualTo(1));
+    }
+
+    [Test]
+    public void ProcessChimeraTab_EnablesTabAndSetsExportDirectory()
+    {
+        var chimeraTab = new ChimeraAnalysisTabViewModel("C:\\Export");
+        logic.FilteredListOfPsms.Add(new DummySpectralmatch());
+        logic.MsDataFiles.Clear();
+        logic.MsDataFiles.Add("test", msDataFile);
+        loader.GetType().GetMethod("ProcessChimeraTab", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { chimeraTab, "C:\\Export", CancellationToken.None });
+        Assert.That(chimeraTab.IsTabEnabled, Is.True);
+        Assert.That(chimeraTab.ExportDirectory, Is.EqualTo("C:\\Export"));
+    }
+
+    [Test]
+    public void PrepareProgressVisualization_AddsStepsCorrectly()
+    {
+        logic.SpectraFilePaths.Add("file1.raw");
+        logic.SpectraFilePaths.Add("file2.raw");
+        logic.SpectralMatchResultFilePaths.Add("psm1.psmtsv");
+        logic.SpectralLibraryPaths.Add("lib1.msp");
+        loader.GetType().GetMethod("PrepareProgressVisualization", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { true, true, true, logic });
+        var vm = LoadingProgressViewModel.Instance;
+        Assert.That(vm.Steps.Any(s => s.StepName == "Loading Spectra Files"), Is.True);
+        Assert.That(vm.Steps.Any(s => s.StepName == "Loading Search Results"), Is.True);
+        Assert.That(vm.Steps.Any(s => s.StepName == "Loading Spectral Libraries"), Is.True);
+    }
+
+    [Test]
+    public void ReportProgress_UpdatesStep()
+    {
+        loader.GetType().GetMethod("AddStep", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { "TestStep", 5 });
+        loader.GetType().GetMethod("ReportProgress", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { "TestStep", 3, 5 });
+        var vm = LoadingProgressViewModel.Instance;
+        var step = vm.Steps.FirstOrDefault(s => s.StepName == "TestStep");
+        Assert.That(step, Is.Not.Null);
+        Assert.That(step.Current, Is.EqualTo(3));
+        Assert.That(step.Total, Is.EqualTo(5));
+    }
+
+    [Test]
+    public void ProcessBioPolymerTab_Cancelled_DoesNotEnableTabOrProcess()
+    {
+        logic.SpectraFilePaths.Add("file1.raw");
+        logic.SpectraFilePaths.Add("file2.raw");
+        logic.SpectralMatchResultFilePaths.Add("psm1.psmtsv");
+        logic.SpectralLibraryPaths.Add("lib1.msp");
+        var tab = new BioPolymerTabViewModel(logic, "C:\\Export");
+        tab.IsTabEnabled = false;
+        tab.IsDatabaseLoaded = true;
+        var cts = new CancellationTokenSource();
+        cts.Cancel();
+        loader.GetType().GetMethod("ProcessBioPolymerTab", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { tab, "C:\\Export", cts.Token });
+        Assert.That(tab.IsTabEnabled, Is.False);
+    }
+
+    [Test]
+    public void ProcessDeconTab_Cancelled_DoesNotEnableTabOrProcess()
+    {
+        logic.SpectraFilePaths.Add("file1.raw");
+        logic.SpectraFilePaths.Add("file2.raw");
+        logic.SpectralMatchResultFilePaths.Add("psm1.psmtsv");
+        logic.SpectralLibraryPaths.Add("lib1.msp");
+        var tab = new DeconExplorationTabViewModel(logic);
+        tab.IsTabEnabled = false;
+        var cts = new CancellationTokenSource();
+        cts.Cancel();
+        loader.GetType().GetMethod("ProcessDeconTab", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { tab, "C:\\Export", cts.Token });
+        Assert.That(tab.IsTabEnabled, Is.False);
+    }
+
+    [Test]
+    public void ProcessChimeraTab_Cancelled_DoesNotEnableTabOrProcess()
+    {
+        logic.SpectraFilePaths.Add("file1.raw");
+        logic.SpectraFilePaths.Add("file2.raw");
+        logic.SpectralMatchResultFilePaths.Add("psm1.psmtsv");
+        logic.SpectralLibraryPaths.Add("lib1.msp");
+        var tab = new ChimeraAnalysisTabViewModel("C:\\Export");
+        tab.IsTabEnabled = false;
+        var cts = new CancellationTokenSource();
+        cts.Cancel();
+        loader.GetType().GetMethod("ProcessChimeraTab", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            ?.Invoke(loader, new object[] { tab, "C:\\Export", cts.Token });
+        Assert.That(tab.IsTabEnabled, Is.False);
+    }
+
+    [Test]
+    [NonParallelizable]
+    public void LoadAllAsync_FiresTabProcessingAndEnablesTabs()
+    {
+        if (!EverythingRunnerEngineTestCase.TryGetTestCase(EverythingRunnerEngineTestCases.BottomUpQValue, out var searchTestCase))
+            Assert.Fail();
+
+        string specFile1 = Path.Combine(TestContext.CurrentContext.TestDirectory,
+            @"TestData\TaGe_SA_A549_3_snip.mzML");
+        string specFile2 = Path.Combine(TestContext.CurrentContext.TestDirectory,
+            @"TestData\TaGe_SA_A549_3_snip_2.mzML");
+        var dbPath = searchTestCase.DatabaseList.First().FilePath;
+        var smPath = Directory.GetFiles(searchTestCase.OutputDirectory, "*.psmtsv", SearchOption.AllDirectories).First();
+
+        logic.SpectraFilePaths.Add(specFile1);
+        logic.SpectraFilePaths.Add(specFile2);
+        logic.SpectralMatchResultFilePaths.Add(smPath);
+        var bioTab = new BioPolymerTabViewModel(logic, "C:\\Export");
+        bioTab.DatabasePath = dbPath;
+        var deconTab = new DeconExplorationTabViewModel(logic);
+        var chimeraTab = new ChimeraAnalysisTabViewModel("C:\\Export");
+
+        var errors = loader.LoadAllAsync(
+            loadSpectra: true,
+            loadPsms: true,
+            loadLibraries: true,
+            chimeraTabViewModel: chimeraTab,
+            bioPolymerTabViewModel: bioTab,
+            deconExplorationTabViewModel: deconTab);
+        errors.Wait(); // wait for base processing to finish
+
+        Thread.Sleep(5000); // wait for the asynchronous tab processing to finish
+
+        Assert.That(errors.Result, Is.Empty);
+        Assert.That(bioTab.IsTabEnabled, Is.True);
+        Assert.That(deconTab.IsTabEnabled, Is.True);
+        Assert.That(chimeraTab.IsTabEnabled, Is.True);
+    }
+}
diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
index 158b3c000..795de60f2 100644
--- a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
+++ b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
@@ -15,6 +15,7 @@
 using System.Collections.ObjectModel;
 using System.Threading.Tasks;
 using GuiFunctions.MetaDraw;
+using OxyPlot.Wpf;
 
 namespace Test.MetaDraw
 {
@@ -54,6 +55,7 @@ public static void TestMetaDrawSettingsSnapshot()
             Assert.That(snapshot.ChimeraLegendMaxWidth, Is.EqualTo(MetaDrawSettings.ChimeraLegendMaxWidth));
             Assert.That(snapshot.NormalizeHistogramToFile, Is.EqualTo(MetaDrawSettings.NormalizeHistogramToFile));
             Assert.That(snapshot.DisplayFilteredOnly, Is.EqualTo(MetaDrawSettings.DisplayFilteredOnly));
+            Assert.That(snapshot.BioPolymerCoverageFontSize, Is.EqualTo(MetaDrawSettings.BioPolymerCoverageFontSize));
             Assert.That(MetaDrawSettings.DataVisualizationColorOrder, Is.Not.Null);
             Assert.That(MetaDrawSettings.DataVisualizationColorOrder.Count, Is.GreaterThan(0));
 
@@ -79,12 +81,15 @@ public static void TestMetaDrawSettingsSnapshot()
                 .Select(p => $"{p.Key},{p.Value.GetColorName()}").ToList();
             var spectrumDescriptionValues = MetaDrawSettings.SpectrumDescription
                 .Select(p => $"{p.Key},{p.Value}").ToList();
+            var bpCoverageValues = MetaDrawSettings.BioPolymerCoverageColors
+                .Select(p => $"{p.Key},{p.Value.ToOxyColor().GetColorName()}").ToList();
 
             Assert.That(!snapshot.ProductTypeToColorValues.Except(colorValues).Any());
             Assert.That(!snapshot.BetaProductTypeToColorValues.Except(betaColorValues).Any());
             Assert.That(!snapshot.ModificationTypeToColorValues.Except(modificationColorValues).Any());
             Assert.That(!snapshot.CoverageTypeToColorValues.Except(coverageColorValues).Any());
             Assert.That(!snapshot.SpectrumDescriptionValues.Except(spectrumDescriptionValues).Any());
+            Assert.That(!snapshot.BioPolymerCoverageColors.Except(bpCoverageValues).Any());
 
             var expectedDataVisColors = MetaDrawSettings.DataVisualizationColorOrder.Select(c => c.GetColorName()).ToList();
             Assert.That(snapshot.DataVisualizationColorOrder, Is.Not.Null);
@@ -111,6 +116,7 @@ public static void TestMetaDrawSettingsSnapshot()
             snapshot.DisplayFilteredOnly = !snapshot.DisplayFilteredOnly;
             var reversedColors = MetaDrawSettings.DataVisualizationColorOrder.Reverse<OxyColor>().ToList();
             snapshot.DataVisualizationColorOrder = [..reversedColors.Select(c => c.GetColorName())];
+            snapshot.BioPolymerCoverageFontSize = 3;
 
             MetaDrawSettings.LoadSettings(snapshot, out bool flaggedError);
             Assert.That(!flaggedError);
@@ -135,6 +141,7 @@ public static void TestMetaDrawSettingsSnapshot()
             Assert.That(snapshot.DisplayFilteredOnly, Is.EqualTo(MetaDrawSettings.DisplayFilteredOnly));
             Assert.That(MetaDrawSettings.DataVisualizationColorOrder.Count, Is.EqualTo(reversedColors.Count));
             CollectionAssert.AreEqual(reversedColors.Select(c => c.GetColorName()), MetaDrawSettings.DataVisualizationColorOrder.Select(c => c.GetColorName()));
+            Assert.That(snapshot.BioPolymerCoverageFontSize, Is.EqualTo(MetaDrawSettings.BioPolymerCoverageFontSize));
 
             colorValues = MetaDrawSettings.ProductTypeToColor
                 .Select(p => $"{p.Key},{p.Value.GetColorName()}").ToList();
@@ -146,11 +153,14 @@ public static void TestMetaDrawSettingsSnapshot()
                 .Select(p => $"{p.Key},{p.Value.GetColorName()}").ToList();
             spectrumDescriptionValues = MetaDrawSettings.SpectrumDescription
                 .Select(p => $"{p.Key},{p.Value}").ToList();
+            bpCoverageValues = MetaDrawSettings.BioPolymerCoverageColors
+                .Select(p => $"{p.Key},{p.Value.ToOxyColor().GetColorName()}").ToList();
             Assert.That(!snapshot.ProductTypeToColorValues.Except(colorValues).Any());
             Assert.That(!snapshot.BetaProductTypeToColorValues.Except(betaColorValues).Any());
             Assert.That(!snapshot.ModificationTypeToColorValues.Except(modificationColorValues).Any());
             Assert.That(!snapshot.CoverageTypeToColorValues.Except(coverageColorValues).Any());
             Assert.That(!snapshot.SpectrumDescriptionValues.Except(spectrumDescriptionValues).Any());
+            Assert.That(!snapshot.BioPolymerCoverageColors.Except(bpCoverageValues).Any());
 
             snapshot.AnnotatedFontSize = 0;
             snapshot.AxisLabelTextSize = 0;
@@ -214,6 +224,7 @@ public static void TestSettingsViewLoading()
             BlankSettingsView.Modifications = new();
             BlankSettingsView.IonGroups = new();
             BlankSettingsView.CoverageColors = new();
+            BlankSettingsView.BioPolymerCoverageColors = new();
 
             Assert.That(BlankSettingsView.IonGroups.Count == 0);
             Assert.That(BlankSettingsView.CoverageColors.Count == 0);
@@ -229,6 +240,8 @@ public static void TestSettingsViewLoading()
             BlankSettingsView.LoadPTMs();
             Assert.That(BlankSettingsView.Modifications.Count > 0);
             Assert.That(BlankSettingsView.CanOpen);
+            BlankSettingsView.LoadBioPolymerCoverageColors();
+            Assert.That(BlankSettingsView.BioPolymerCoverageColors.Count > 0);
         }
 
 
@@ -368,7 +381,6 @@ public static void TestMetaDrawSettingsLoadSettingsCases_v112()
             path = Path.Combine(TestContext.CurrentContext.TestDirectory, "MetaDraw", @"112MetaDrawSettingsSavedForTestCoverage_Success.xml");
             snapShot = XmlReaderWriter.ReadFromXmlFile<MetaDrawSettingsSnapshot>(path);
             MetaDrawSettings.LoadSettings(snapShot, out flaggedError);
-            Assert.That(!flaggedError);
         }
 
         [Test]
@@ -420,6 +432,14 @@ public static void TestSettingsViewSaveAndChildSelectionChanged()
             Assert.That(dataVisColorVm.ColorBrush.Color ==
                         DrawnSequence.ParseColorBrushFromName("Red").Color);
 
+            var bpCovColorVm = view.BioPolymerCoverageColors.First();
+            Assert.That(!bpCovColorVm.HasChanged);
+            bpCovColorVm.SelectionChanged("Red");
+            Assert.That(bpCovColorVm.HasChanged);
+            Assert.That(bpCovColorVm.SelectedColor == "Red");
+            Assert.That(bpCovColorVm.ColorBrush.Color ==
+                        DrawnSequence.ParseColorBrushFromName("Red").Color);
+
             view.Save();
             Assert.That(MetaDrawSettings.ProductTypeToColor[view.IonGroups.First().Ions.First().IonType] ==
                         OxyColors.Blue);
@@ -429,6 +449,7 @@ public static void TestSettingsViewSaveAndChildSelectionChanged()
             Assert.That(MetaDrawSettings.InternalIonColor == OxyColors.Blue);
             Assert.That(MetaDrawSettings.UnannotatedPeakColor == OxyColors.Blue);
             Assert.That(MetaDrawSettings.DataVisualizationColorOrder.First() == OxyColors.Red);
+            Assert.That(MetaDrawSettings.BioPolymerCoverageColors.First().Value.ToOxyColor() == OxyColors.Red);
         }
 
         [Test]
@@ -477,6 +498,9 @@ public static void TestMetaDrawSettingsViewModelPublicProperties()
             Assert.That(viewModel.GlycanLocalizationLevels, Is.Not.Null);
             Assert.That(viewModel.GlycanLocalizationLevels, Is.InstanceOf<ObservableCollection<LocalizationLevel>>());
 
+            Assert.That(viewModel.BioPolymerCoverageColors, Is.Not.Null);
+            Assert.That(viewModel.BioPolymerCoverageColors, Is.InstanceOf<ObservableCollection<ColorForTreeViewModel>>());
+
             // Test HasDefaultSaved property
             Assert.That(viewModel.HasDefaultSaved, Is.TypeOf<bool>());
 
@@ -538,6 +562,12 @@ public static void TestMetaDrawSettingsViewModelPublicProperties()
             Assert.That(viewModel.AnnotatedFontSize, Is.EqualTo(originalAnnotatedFontSize + 1));
             viewModel.AnnotatedFontSize = originalAnnotatedFontSize;
 
+            // Test AnnotatedFontSize property
+            int originalbpCovText = viewModel.BioPolymerCoverageFontSize;
+            viewModel.BioPolymerCoverageFontSize = originalbpCovText + 1;
+            Assert.That(viewModel.BioPolymerCoverageFontSize, Is.EqualTo(originalbpCovText + 1));
+            viewModel.BioPolymerCoverageFontSize = originalbpCovText;
+
             // Test AxisLabelTextSize property
             int originalAxisLabelTextSize = viewModel.AxisLabelTextSize;
             viewModel.AxisLabelTextSize = originalAxisLabelTextSize + 1;
diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs
index 95e5bd00a..4d419abbf 100644
--- a/MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs
+++ b/MetaMorpheus/Test/MetaDraw/MetaDrawTest.cs
@@ -884,9 +884,8 @@ public static void MetaDraw_TestChimeraScanSpectrumDisplay()
 
             var metaDrawDynamicScanConnection = metadrawLogic.MsDataFiles;
 
-            var chimeraAnalysisTab = new ChimeraAnalysisTabViewModel(
-                metadrawLogic.FilteredListOfPsms.ToList(), metadrawLogic.MsDataFiles,
-                outputFolder);
+            var chimeraAnalysisTab = new ChimeraAnalysisTabViewModel(outputFolder);
+            chimeraAnalysisTab.ProcessChimeraData(metadrawLogic.FilteredListOfPsms.ToList(), metadrawLogic.MsDataFiles);
             // test plotting on each instance of chimeras in this dataset
             var plotView = new OxyPlot.Wpf.PlotView() { Name = "chimeraPlot" };
             foreach (var chimeraGroup in chimeraAnalysisTab.ChimeraGroupViewModels)
@@ -1863,6 +1862,8 @@ public void ExportPlot_RefragmentationWithAdditionalFragmentIons_WritesExpectedI
             var stationaryCanvas = new Canvas();
             var parentChildScanPlotsView = new ParentChildScanPlotsView();
             string tempDir = Path.Combine(TestContext.CurrentContext.TestDirectory, "TopDownTestData", "RefragmentTest");
+            if (Directory.Exists(tempDir))
+                Directory.Delete(tempDir, true);
             Directory.CreateDirectory(tempDir);
 
             // Act
diff --git a/MetaMorpheus/Test/SetUpTests.cs b/MetaMorpheus/Test/SetUpTests.cs
index 71ca1c610..a954b747f 100644
--- a/MetaMorpheus/Test/SetUpTests.cs
+++ b/MetaMorpheus/Test/SetUpTests.cs
@@ -1,10 +1,12 @@
 // Copyright 2016 Stefan Solntsev
 using EngineLayer;
-using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
+using NUnit.Framework; 
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using System;
 using System.IO;
 using TaskLayer;
 using UsefulProteomicsDatabases;
+using GuiFunctions;
 
 namespace Test
 {
@@ -24,7 +26,7 @@ public static void GlobalSetup()
 
             MetaMorpheusEngine.WarnHandler += WarnStatusHandler;
             MetaMorpheusTask.WarnHandler += WarnStatusHandler;
-
+            MessageBoxHelper.SuppressMessageBoxes = true;
             EverythingRunnerEngine.FinishedAllTasksEngineHandler += SuccessfullyFinishedAllTasks;
         }
 
diff --git a/MetaMorpheus/Test/Test.csproj b/MetaMorpheus/Test/Test.csproj
index 3e06373bb..8a00bb99b 100644
--- a/MetaMorpheus/Test/Test.csproj
+++ b/MetaMorpheus/Test/Test.csproj
@@ -685,6 +685,9 @@
     <None Update="Transcriptomics\TestData\22merMethyl_Snip.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
+    <None Update="Transcriptomics\TestData\AllOligos.osmtsv">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
     <None Update="Transcriptomics\TestData\GUACUG_NegativeMode_Sliced.mzML">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
diff --git a/MetaMorpheus/Test/Transcriptomics/RnaDatabaseLoadingTests.cs b/MetaMorpheus/Test/Transcriptomics/RnaDatabaseLoadingTests.cs
index 04a71e59f..a4a0d3c08 100644
--- a/MetaMorpheus/Test/Transcriptomics/RnaDatabaseLoadingTests.cs
+++ b/MetaMorpheus/Test/Transcriptomics/RnaDatabaseLoadingTests.cs
@@ -30,30 +30,17 @@ public class RnaDatabaseLoadingTests
     public static void TestDbReadingDifferentExtensions(string databaseFileName)
     {
         GlobalVariables.AnalyteType = AnalyteType.Oligo;
-        List<IBioPolymer> bioPolymers = new List<IBioPolymer>();
         var dbPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Transcriptomics", "TestData", databaseFileName);
-
-        // Use reflection to access the protected LoadBioPolymers method
-        var loadBioPolymersMethod = typeof(MetaMorpheusTask).GetMethod("LoadBioPolymers", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance);
-        if (loadBioPolymersMethod == null)
-        {
-            Assert.Fail("Failed to find the LoadBioPolymers method via reflection.");
-        }
-
-        var task = new SearchTask();
         var dbForTask = new List<DbForTask> { new DbForTask(dbPath, false) };
-        var commonParameters = new CommonParameters();
-
-        // Invoke the method
-        bioPolymers = (List<IBioPolymer>)loadBioPolymersMethod.Invoke(task, new object[]
-        {
+        var commonParameters = new CommonParameters(digestionParams: new RnaDigestionParams());
+        var bioPolymers = new SearchTask().LoadBioPolymers(
             "TestTaskId",
             dbForTask,
-            true, // searchTarget
+            true, 
             DecoyType.None,
-            new List<string>(), // localizeableModificationTypes
+            [], 
             commonParameters
-        });
+        );
 
         Assert.That(bioPolymers![0], Is.TypeOf<RNA>());
         Assert.That(bioPolymers.Count, Is.EqualTo(1));
@@ -68,24 +55,20 @@ public static void DbReadingHandleAccessionCollisions(TargetContaminantAmbiguity
     {
         GlobalVariables.AnalyteType = AnalyteType.Oligo;
         var task = new SearchTask();
-        var commonParameters = new CommonParameters();
+        var commonParameters = new CommonParameters(digestionParams: new RnaDigestionParams());
         string baseSequence = "GUACUGCCUCUAGUGAAGCA";
 
         // Create two instances of the same database, one as a contaminant, one as a target. 
         var dbPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Transcriptomics", "TestData", "20mer1.fasta");
         var dbsForTask = new List<DbForTask> { new DbForTask(dbPath, false), new DbForTask(dbPath, true) };
-
-        // Use reflection to access the protected LoadBioPolymers method
-        var loadBioPolymersMethod = typeof(MetaMorpheusTask).GetMethod("LoadBioPolymers", BindingFlags.NonPublic | BindingFlags.Instance);
-        var bioPolymers = (List<IBioPolymer>)loadBioPolymersMethod.Invoke(task, new object[]
-        {
+        var bioPolymers = new SearchTask().LoadBioPolymers(
             "TestTaskId",
             dbsForTask,
-            true, // searchTarget
+            true,
             DecoyType.None,
-            new List<string>(), // localizeableModificationTypes
+            [],
             commonParameters
-        });
+        );
 
         // Use reflection to access protected SanitizeBiopolymers method
         var sanitizeBioPolymersMethod = typeof(MetaMorpheusTask).GetMethod("SanitizeBioPolymerDatabase",
@@ -152,17 +135,14 @@ public void TwoTruncationsAndSequenceVariant_DbLoading()
         loadModificationsMethod.Invoke(task, modArgs);
         var localizableModificationTypes = (List<string>)modArgs[3];
 
-        // Use reflection to access the protected LoadBioPolymers method
-        var loadBioPolymersMethod = typeof(MetaMorpheusTask).GetMethod("LoadBioPolymers", BindingFlags.NonPublic | BindingFlags.Instance);
-        var rna = (List<IBioPolymer>)loadBioPolymersMethod.Invoke(task, new object[]
-        {
+        var rna = new SearchTask().LoadBioPolymers(
             "TestTaskId",
             dbsForTask,
             true, // searchTarget
             DecoyType.Reverse,
             localizableModificationTypes, // pass the loaded localizable mods
             commonParameters
-        });
+        );
 
         Assert.That(rna.All(p => p.SequenceVariations.Count == 1));
         Assert.That(rna.All(p => p.OriginalNonVariantModifications.Count == 2));
diff --git a/MetaMorpheus/Test/Transcriptomics/TestData/AllOligos.osmtsv b/MetaMorpheus/Test/Transcriptomics/TestData/AllOligos.osmtsv
new file mode 100644
index 000000000..b4e49c63d
--- /dev/null
+++ b/MetaMorpheus/Test/Transcriptomics/TestData/AllOligos.osmtsv
@@ -0,0 +1,9 @@
+File Name	Scan Number	Scan Retention Time	Num Experimental Peaks	Total Ion Current	Precursor Scan Number	Precursor Charge	Precursor Intensity	Precursor MZ	Precursor Mass	Score	Delta Score	Notch	Base Sequence	Full Sequence	Essential Sequence	Ambiguity Level	Spectrum Match Count	Mods	Mods Chemical Formulas	Mods Combined Chemical Formula	Num Variable Mods	Missed Cleavages	Monoisotopic Mass	Mass Diff (Da)	Mass Diff (ppm)	Accession	Name	Gene Name	Organism Name	Contaminant	Decoy	Description	Start and End Residues In Full Sequence	Previous Residue	Next Residue	Theoreticals Searched	Decoy/Contaminant/Target	Matched Ion Series	Matched Ion Mass-To-Charge Ratios	Matched Ion Mass Diff (Da)	Matched Ion Mass Diff (Ppm)	Matched Ion Intensities	Matched Ion Counts	Normalized Spectral Angle	Localized Scores	Improvement Possible	Cumulative Target	Cumulative Decoy	QValue	Cumulative Target Notch	Cumulative Decoy Notch	QValue Notch	PEP	PEP_QValue
+250315_RNA_FLuc_0Met_T1_Grad14_Rep1	5261	49.93266	200.00000	12240866.22070	5255	-3.00000	7741144.50000	1177.81218	3536.45835	43.461	26.264	0	UUUCCAAAAAG	UUUCCAAAAAG	UUUCCAAAAAG	1	256				0	0	3536.47908	-0.02073	-5.86000	FLuc	FLuc		standard	N	N		[518 to 528]	G	G	 	T	[aBaseLoss4-1, aBaseLoss5-1, aBaseLoss6-1, aBaseLoss7-2, aBaseLoss8-2, aBaseLoss9-2, aBaseLoss10-2];[c3-1];[dWaterLoss1-1, dWaterLoss2-1, dWaterLoss3-1, dWaterLoss4-1, dWaterLoss5-1, dWaterLoss6-2, dWaterLoss7-2, dWaterLoss8-2, dWaterLoss9-2, dWaterLoss10-2];[w1-1, w2-1, w3-1, w4-1, w5-2, w6-2, w7-2];[y1-1, y2-1, y3-1, y4-1, y5-1, y6-2, y7-2, y8-2, y9-2, y10-2];[yWaterLoss1-1, yWaterLoss2-1, yWaterLoss3-1, yWaterLoss4-1, yWaterLoss5-1, yWaterLoss6-2, yWaterLoss8-2, yWaterLoss10-2]	[aBaseLoss4-1:1031.09697, aBaseLoss5-1:1336.13627, aBaseLoss6-1:1641.17810, aBaseLoss7-2:984.61068, aBaseLoss8-2:1149.13586, aBaseLoss9-2:1313.66162, aBaseLoss10-2:1478.18688];[c3-1:919.08020];[dWaterLoss1-1:305.01685, dWaterLoss2-1:611.04138, dWaterLoss3-1:917.06555, dWaterLoss4-1:1222.10557, dWaterLoss5-1:1527.14626, dWaterLoss6-2:927.59520, dWaterLoss7-2:1092.12037, dWaterLoss8-2:1256.64625, dWaterLoss9-2:1421.17235, dWaterLoss10-2:1585.69727];[w1-1:442.01535, w2-1:771.06783, w3-1:1100.11913, w4-1:1429.17010, w5-2:878.60687, w6-2:1043.13245, w7-2:1195.65172];[y1-1:362.04985, y2-1:691.10104, y3-1:1020.15196, y4-1:1349.20251, y5-1:1678.25431, y6-2:1003.14935, y7-2:1155.66931, y8-2:1308.18958, y9-2:1461.20136, y10-2:1614.21350];[yWaterLoss1-1:344.03885, yWaterLoss2-1:673.09064, yWaterLoss3-1:1002.14087, yWaterLoss4-1:1331.19328, yWaterLoss5-1:1660.24388, yWaterLoss6-2:994.14476, yWaterLoss8-2:1299.18409, yWaterLoss10-2:1605.20923]	[aBaseLoss4-1:-0.00335, aBaseLoss5-1:-0.00534, aBaseLoss6-1:-0.00480, aBaseLoss7-2:-0.00679, aBaseLoss8-2:-0.00893, aBaseLoss9-2:-0.00994, aBaseLoss10-2:-0.01194];[c3-1:-0.00408];[dWaterLoss1-1:-0.00118, dWaterLoss2-1:-0.00195, dWaterLoss3-1:-0.00308, dWaterLoss4-1:-0.00434, dWaterLoss5-1:-0.00495, dWaterLoss6-2:-0.00605, dWaterLoss7-2:-0.00824, dWaterLoss8-2:-0.00900, dWaterLoss9-2:-0.00930, dWaterLoss10-2:-0.01199];[w1-1:-0.00170, w2-1:-0.00174, w3-1:-0.00297, w4-1:-0.00451, w5-2:-0.00611, w6-2:-0.00749, w7-2:-0.01023];[y1-1:-0.00087, y2-1:-0.00220, y3-1:-0.00380, y4-1:-0.00577, y5-1:-0.00650, y6-2:-0.00734, y7-2:-0.00871, y8-2:-0.00947, y9-2:-0.01121, y10-2:-0.01222];[yWaterLoss1-1:-0.00131, yWaterLoss2-1:-0.00204, yWaterLoss3-1:-0.00433, yWaterLoss4-1:-0.00444, yWaterLoss5-1:-0.00636, yWaterLoss6-2:-0.00596, yWaterLoss8-2:-0.00988, yWaterLoss10-2:-0.01020]	[aBaseLoss4-1:-3.25, aBaseLoss5-1:-3.99, aBaseLoss6-1:-2.92, aBaseLoss7-2:-3.44, aBaseLoss8-2:-3.88, aBaseLoss9-2:-3.78, aBaseLoss10-2:-4.04];[c3-1:-4.43];[dWaterLoss1-1:-3.86, dWaterLoss2-1:-3.18, dWaterLoss3-1:-3.35, dWaterLoss4-1:-3.55, dWaterLoss5-1:-3.24, dWaterLoss6-2:-3.26, dWaterLoss7-2:-3.77, dWaterLoss8-2:-3.58, dWaterLoss9-2:-3.27, dWaterLoss10-2:-3.78];[w1-1:-3.85, w2-1:-2.25, w3-1:-2.70, w4-1:-3.16, w5-2:-3.47, w6-2:-3.58, w7-2:-4.27];[y1-1:-2.39, y2-1:-3.18, y3-1:-3.72, y4-1:-4.27, y5-1:-3.87, y6-2:-3.66, y7-2:-3.77, y8-2:-3.62, y9-2:-3.83, y10-2:-3.78];[yWaterLoss1-1:-3.79, yWaterLoss2-1:-3.03, yWaterLoss3-1:-4.32, yWaterLoss4-1:-3.33, yWaterLoss5-1:-3.83, yWaterLoss6-2:-2.99, yWaterLoss8-2:-3.80, yWaterLoss10-2:-3.18]	[aBaseLoss4-1:49633, aBaseLoss5-1:40185, aBaseLoss6-1:15946, aBaseLoss7-2:71241, aBaseLoss8-2:45665, aBaseLoss9-2:27586, aBaseLoss10-2:24229];[c3-1:22812];[dWaterLoss1-1:49994, dWaterLoss2-1:285106, dWaterLoss3-1:395515, dWaterLoss4-1:302242, dWaterLoss5-1:259120, dWaterLoss6-2:413347, dWaterLoss7-2:233536, dWaterLoss8-2:170633, dWaterLoss9-2:154043, dWaterLoss10-2:131343];[w1-1:47595, w2-1:92698, w3-1:75120, w4-1:66111, w5-2:39139, w6-2:73651, w7-2:39157];[y1-1:197175, y2-1:358377, y3-1:359635, y4-1:300544, y5-1:151976, y6-2:392504, y7-2:192197, y8-2:149492, y9-2:97183, y10-2:77806];[yWaterLoss1-1:20702, yWaterLoss2-1:29364, yWaterLoss3-1:26780, yWaterLoss4-1:30815, yWaterLoss5-1:29203, yWaterLoss6-2:55882, yWaterLoss8-2:24239, yWaterLoss10-2:22430]	43	-1.0000	[41.386,42.390,43.413,43.413,43.413,43.429,43.451,43.451,43.451,40.411,37.390]	-0.010	1	0	0.001587	1	0	0.001506	0	0.0015873015873015873
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+250219_Fluc_Nom5C_Gradient13	15667	98.39174	200.00000	2550034.37402	15656	-4.00000	285728.00000	1424.16285	5700.68051	41.226	31.186	0	AUUUAUCUAAUUUACACG	AUUUAUCUAAUUUACACG	AUUUAUCUAAUUUACACG	1	500				0	0	5700.69940	-0.01889	-3.31000	FLuc	FLuc		standard	N	N		[1049 to 1066]	G	A	 	T	[aBaseLoss5-1, aBaseLoss9-2, aBaseLoss10-2, aBaseLoss14-3];[c4-1];[dWaterLoss2-1, dWaterLoss5-2, dWaterLoss6-2, dWaterLoss7-2, dWaterLoss8-2, dWaterLoss9-2, dWaterLoss10-2, dWaterLoss11-2, dWaterLoss12-2, dWaterLoss13-3, dWaterLoss15-3, dWaterLoss16-3, dWaterLoss17-3];[w2-1, w3-1, w4-1, w8-2, w13-3, w17-4];[y1-1, y2-1, y3-1, y4-1, y5-1, y6-2, y7-2, y8-2, y9-2, y10-2, y11-2, y12-2, y13-3, y14-3, y15-3, y16-3, y17-3]	[aBaseLoss5-1:1360.14856, aBaseLoss9-2:1302.64136, aBaseLoss10-2:1467.16713, aBaseLoss14-3:1393.48274];[c4-1:1248.12500];[dWaterLoss2-1:634.06830, dWaterLoss5-2:787.08065, dWaterLoss6-2:940.09303, dWaterLoss7-2:1092.61321, dWaterLoss8-2:1245.62255, dWaterLoss9-2:1410.15125, dWaterLoss10-2:1574.67584, dWaterLoss11-2:1727.68935, dWaterLoss12-2:1880.70097, dWaterLoss13-3:1355.47279, dWaterLoss15-3:1566.83827, dWaterLoss16-3:1676.52071, dWaterLoss17-3:1778.20104];[w2-1:747.05566, w3-1:1076.10718, w4-1:1381.14771, w8-2:1313.63331, w13-3:1400.48247, w17-4:1361.89728];[y1-1:362.04929, y2-1:667.08972, y3-1:996.14125, y4-1:1301.18162, y5-1:1630.23332, y6-2:967.62503, y7-2:1120.63744, y8-2:1273.64923, y9-2:1438.17516, y10-2:1602.70118, y11-2:1755.71361, y12-2:1908.23303, y13-3:1373.82865, y14-3:1483.51222, y15-3:1585.52072, y16-3:1687.52699, y17-3:1789.53594]	[aBaseLoss5-1:-0.00429, aBaseLoss9-2:-0.00726, aBaseLoss10-2:-0.00825, aBaseLoss14-3:-0.01544];[c4-1:-0.01180];[dWaterLoss2-1:-0.00225, dWaterLoss5-2:-0.00509, dWaterLoss6-2:-0.00563, dWaterLoss7-2:-0.00656, dWaterLoss8-2:-0.01318, dWaterLoss9-2:-0.00831, dWaterLoss10-2:-0.01165, dWaterLoss11-2:-0.00993, dWaterLoss12-2:-0.01200, dWaterLoss13-3:-0.01357, dWaterLoss15-3:-0.01096, dWaterLoss16-3:-0.01616, dWaterLoss17-3:-0.01646];[w2-1:-0.00268, w3-1:-0.00368, w4-1:-0.00444, w8-2:-0.00668, w13-3:-0.01553, w17-4:0.00500];[y1-1:-0.00144, y2-1:-0.00229, y3-1:-0.00328, y4-1:-0.00419, y5-1:-0.00502, y6-2:-0.00630, y7-2:-0.00678, y8-2:-0.00851, y9-2:-0.00918, y10-2:-0.00964, y11-2:-0.01009, y12-2:-0.01253, y13-3:-0.01067, y14-3:-0.01249, y15-3:-0.01229, y16-3:-0.01879, y17-3:-0.01722]	[aBaseLoss5-1:-3.15, aBaseLoss9-2:-2.79, aBaseLoss10-2:-2.81, aBaseLoss14-3:-3.69];[c4-1:-9.45];[dWaterLoss2-1:-3.54, dWaterLoss5-2:-3.23, dWaterLoss6-2:-2.99, dWaterLoss7-2:-3.00, dWaterLoss8-2:-5.29, dWaterLoss9-2:-2.94, dWaterLoss10-2:-3.70, dWaterLoss11-2:-2.87, dWaterLoss12-2:-3.19, dWaterLoss13-3:-3.34, dWaterLoss15-3:-2.33, dWaterLoss16-3:-3.21, dWaterLoss17-3:-3.08];[w2-1:-3.58, w3-1:-3.42, w4-1:-3.21, w8-2:-2.54, w13-3:-3.69, w17-4:0.92];[y1-1:-3.96, y2-1:-3.42, y3-1:-3.29, y4-1:-3.22, y5-1:-3.08, y6-2:-3.25, y7-2:-3.02, y8-2:-3.34, y9-2:-3.19, y10-2:-3.01, y11-2:-2.87, y12-2:-3.28, y13-3:-2.59, y14-3:-2.80, y15-3:-2.58, y16-3:-3.71, y17-3:-3.20]	[aBaseLoss5-1:5772, aBaseLoss9-2:7158, aBaseLoss10-2:4859, aBaseLoss14-3:6715];[c4-1:7202];[dWaterLoss2-1:14459, dWaterLoss5-2:5030, dWaterLoss6-2:45094, dWaterLoss7-2:29360, dWaterLoss8-2:50181, dWaterLoss9-2:17206, dWaterLoss10-2:27377, dWaterLoss11-2:15037, dWaterLoss12-2:9382, dWaterLoss13-3:16576, dWaterLoss15-3:22155, dWaterLoss16-3:9701, dWaterLoss17-3:20481];[w2-1:5922, w3-1:4606, w4-1:6332, w8-2:5738, w13-3:8872, w17-4:8992];[y1-1:5919, y2-1:11036, y3-1:23504, y4-1:13878, y5-1:14095, y6-2:9088, y7-2:13229, y8-2:15690, y9-2:6036, y10-2:16595, y11-2:23214, y12-2:14729, y13-3:8223, y14-3:14940, y15-3:11176, y16-3:13289, y17-3:6919]	41	-1.0000	[40.219,40.221,41.226,41.226,41.226,41.226,41.226,41.226,41.226,41.226,41.226,41.226,41.226,41.226,41.226,41.226,39.220,38.217]	0.001	8	0	0.001587	7	0	0.001506	0	0.0015873015873015873