diff --git a/CMD/CMD.csproj b/CMD/CMD.csproj
index 471c9f5..2f89c62 100644
--- a/CMD/CMD.csproj
+++ b/CMD/CMD.csproj
@@ -15,7 +15,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.553" />
+    <PackageReference Include="mzLib" Version="8.0.0" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />
diff --git a/GUI/GUI.csproj b/GUI/GUI.csproj
index 1e2c014..1fdb3f0 100644
--- a/GUI/GUI.csproj
+++ b/GUI/GUI.csproj
@@ -15,7 +15,7 @@
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.553" />
+    <PackageReference Include="mzLib" Version="8.0.0" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />
diff --git a/GUI/MainWindow.xaml b/GUI/MainWindow.xaml
index 517f161..14e05e8 100644
--- a/GUI/MainWindow.xaml
+++ b/GUI/MainWindow.xaml
@@ -403,10 +403,10 @@
                         <CheckBox Name="normalizeCheckbox" Content="Normalize Intensities" Foreground="DarkGray" 
                                   Grid.Row="4" Style="{StaticResource SquareCheckbox}" 
                                   ToolTip="Corrects systematic intensity errors with median normalization. The main assumption is that most proteins do not change in abundance between samples" />
-                        
-                        <CheckBox Name="pepQValueCheckbox" Content="Use PEP Q Values" Foreground="DarkGray" 
+
+                        <CheckBox Name="isoTrackCheckbox" Content="IsoTracker: Improved quantification of isobaric species" Foreground="DarkGray" 
                                   Grid.Row="5" Style="{StaticResource SquareCheckbox}" 
-                                  ToolTip="Determines how FlashLFQ chooses which peptides to quantify (only applies to MetaMorpheus identifications). Using PEP Q generally yields more peptide IDs" />         
+                                  ToolTip="Turn on Ray's awesome algorithm!" />
 
                         <CheckBox Name="sharedPeptideCheckbox" Content="Use shared peptides for protein quantification" Foreground="DarkGray" 
                                   Grid.Row="6" 
@@ -448,12 +448,14 @@
                                     <ColumnDefinition Width="300"/>
                                 </Grid.ColumnDefinitions>
 
-                                <CheckBox Name="integrateCheckBox" Content="Integrate Peak Areas" Foreground="DarkGray" Grid.Row="0" Style="{StaticResource SquareCheckbox}"
+                                <CheckBox Name="integrateCheckBox" Grid.Row="0" Content="Integrate Peak Areas" Foreground="DarkGray"  
+                                          Style="{StaticResource SquareCheckbox}"
                                           ToolTip="By default, FlashLFQ reports the peak height and not peak area. Enabling integration reports the peak area"/>
 
-                                <CheckBox Name="precursorIdOnlyCheckbox" Content="Only quantify identified charge" Foreground="DarkGray" Grid.Row="1" Style="{StaticResource SquareCheckbox}"
-                                          ToolTip="FlashLFQ will only quantify the identified charge, and will not look for alternative charges"/>
-
+                                <CheckBox Name="pepQValueCheckbox" Grid.Row="1" Content="Use PEP Q Values" Foreground="DarkGray" 
+                                          Style="{StaticResource SquareCheckbox}" 
+                                          ToolTip="Determines how FlashLFQ chooses which peptides to quantify (only applies to MetaMorpheus identifications). Using PEP Q generally yields more peptide IDs" />
+                                
                                 <StackPanel Orientation="Horizontal" Grid.Row="2" Margin="2"
                                             ToolTip="The mass tolerance in parts per million of isotope peaks (e.g., M+1, M+2 peaks)">
                                     <TextBox Name="isotopePpmToleranceTextBox" Width="40" Foreground="DarkGray" Background="Transparent" BorderBrush="DarkGray" BorderThickness="1" FontSize="13" />
@@ -466,23 +468,27 @@
                                     <Label Content="Number of isotopes required" Foreground="DarkGray" />
                                 </StackPanel>
 
-                                <CheckBox Name="requireMsmsIdInConditionCheckbox" Content="Require MS/MS Identification in Condition" Foreground="DarkGray" Grid.Row="0" 
-                                          Grid.Column="1" Style="{StaticResource SquareCheckbox}" IsEnabled="{Binding IsChecked, ElementName=mbrCheckbox}"
+                                <CheckBox Name="requireMsmsIdInConditionCheckbox" Grid.Row="0" Grid.Column="1" Content="Require MS/MS Identification in Condition" Foreground="DarkGray"  
+                                          Style="{StaticResource SquareCheckbox}" IsEnabled="{Binding IsChecked, ElementName=mbrCheckbox}"
                                           ToolTip="Only try to match peptides from proteins if an MS/MS identified peptide from that protein was observed in the condition"/>
 
-                                <StackPanel Orientation="Horizontal" Grid.Row="1" Grid.Column="1" Margin="2" IsEnabled="{Binding IsChecked, ElementName=mbrCheckbox}"
+                                <CheckBox Name="precursorIdOnlyCheckbox" Grid.Row="1" Grid.Column ="1" Content="Only quantify identified charge" Foreground="DarkGray" 
+                                           Style="{StaticResource SquareCheckbox}"
+                                          ToolTip="FlashLFQ will only quantify the identified charge, and will not look for alternative charges"/>
+
+                                <StackPanel Orientation="Horizontal" Grid.Row="2" Grid.Column="1" Margin="2" IsEnabled="{Binding IsChecked, ElementName=mbrCheckbox}"
                                             ToolTip="The retention-time error allowed in match-between runs. This is not the systematic time shift, but a sort of &quot;variance&quot; or &quot;error&quot; in the retention time allowed">
                                     <TextBox Name="mbrRtWindowTextBox" Width="40" Foreground="DarkGray" Background="Transparent" BorderBrush="DarkGray" BorderThickness="1" FontSize="13" />
                                     <Label Content="Maximum MBR window (minutes)" Foreground="DarkGray" />
                                 </StackPanel>
 
-                                <StackPanel Orientation="Horizontal" Grid.Row="2" Grid.Column="1" Margin="2" IsEnabled="{Binding IsChecked, ElementName=bayesianCheckbox}"
+                                <StackPanel Orientation="Horizontal" Grid.Row="3" Grid.Column="1" Margin="2" IsEnabled="{Binding IsChecked, ElementName=bayesianCheckbox}"
                                             ToolTip="The number of iterations to perform for the Markov-Chain Monte Carlo sampler in the Bayesian stats engine. A larger number of iterations will result in a slower but more precise estimate of the protein fold-change, the PEP, and the FDR">
                                     <TextBox Name="mcmcIterationsTextBox" Width="40" Foreground="DarkGray" Background="Transparent" BorderBrush="DarkGray" BorderThickness="1" FontSize="13" />
                                     <Label Content="MCMC Iterations" Foreground="DarkGray" />
                                 </StackPanel>
 
-                                <StackPanel Orientation="Horizontal" Grid.Row="3" Grid.Column="1" Margin="2" IsEnabled="{Binding IsChecked, ElementName=bayesianCheckbox}"
+                                <StackPanel Orientation="Horizontal" Grid.Row="4" Grid.Column="1" Margin="2" IsEnabled="{Binding IsChecked, ElementName=bayesianCheckbox}"
                                             ToolTip="The seed for the random number generator in the Markov-Chain Monte Carlo sampler. You should probably not change this unless unless you are trying to reproduce an analysis">
                                     <TextBox Name="mcmcRandomSeedTextBox" Width="40" Foreground="DarkGray" Background="Transparent" BorderBrush="DarkGray" BorderThickness="1" FontSize="13" />
                                     <Label Content="MCMC Random Seed" Foreground="DarkGray" />
diff --git a/GUI/MainWindow.xaml.cs b/GUI/MainWindow.xaml.cs
index 51cd844..fa16489 100644
--- a/GUI/MainWindow.xaml.cs
+++ b/GUI/MainWindow.xaml.cs
@@ -82,6 +82,7 @@ private void PopulateSettings()
             ppmToleranceTextBox.Text = settings.PpmTolerance.ToString("F1");
             normalizeCheckbox.IsChecked = settings.Normalize;
             mbrCheckbox.IsChecked = settings.MatchBetweenRuns;
+            isoTrackCheckbox.IsChecked = settings.IsoTracker;
             mbrFDRTextBox.Text = "0.01";
             sharedPeptideCheckbox.IsChecked = settings.UseSharedPeptidesForProteinQuant;
             pepQValueCheckbox.IsChecked = settings.UsePepQValue;
@@ -150,6 +151,8 @@ private void ParseSettings()
             settings.ProteinQuantBaseCondition = (string)ControlConditionComboBox.SelectedItem;
             settings.RequireMsmsIdInCondition = requireMsmsIdInConditionCheckbox.IsChecked.Value;
 
+            settings.IsoTracker = isoTrackCheckbox.IsChecked.Value;
+
             // isotope PPM tolerance
             if (double.TryParse(isotopePpmToleranceTextBox.Text, NumberStyles.Number, CultureInfo.InvariantCulture, out double isotopePpmTolerance))
             {
@@ -442,6 +445,7 @@ private void Run_Click(object sender, RoutedEventArgs e)
                 identFilesDataGrid.IsReadOnly = true;
                 ppmToleranceTextBox.IsEnabled = false;
                 normalizeCheckbox.IsEnabled = false;
+                isoTrackCheckbox.IsEnabled = false;
                 mbrCheckbox.IsEnabled = false;
                 MbrFdrPanel.IsEnabled = false;
                 sharedPeptideCheckbox.IsEnabled = false;
diff --git a/Test/Test.csproj b/Test/Test.csproj
index 5489bd5..a21f0fb 100644
--- a/Test/Test.csproj
+++ b/Test/Test.csproj
@@ -12,7 +12,7 @@
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.553" />
+    <PackageReference Include="mzLib" Version="8.0.0" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="nunit" Version="4.2.2" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.6.0" />
diff --git a/Util/FlashLfqSettings.cs b/Util/FlashLfqSettings.cs
index f2bb92f..f4c5391 100644
--- a/Util/FlashLfqSettings.cs
+++ b/Util/FlashLfqSettings.cs
@@ -87,14 +87,16 @@ public class FlashLfqSettings
 
         [Option("rns", HelpText = "int; random seed for the Bayesian protein fold-change analysis")]
         public int? RandomSeed { get; set; }
-        //TODO: paired samples
 
         [Option("pipfdr", HelpText = "double; fdr cutoff for pip")]
-        public double MbrDetectionQValueThreshold  { get; set; }
+        public double MbrDetectionQValueThreshold { get; set; }
 
         [Option("usepepq", Default = false, HelpText = "bool; determines whether PEP Q Value should be used to determine which peptides to quantify")]
         public bool UsePepQValue { get; set; }
 
+        [Option("isoTrack", Default = false, HelpText = "bool; determines whether IsoTracker should be used to aid in the quantification of isobaric peptides")]
+        public bool IsoTracker { get; set; }
+
         public FlashLfqSettings()
         {
             FlashLfqEngine f = new FlashLfqEngine(new List<Identification>());
@@ -120,6 +122,7 @@ public FlashLfqSettings()
             McmcSteps = f.McmcSteps;
             McmcBurninSteps = f.McmcBurninSteps;
             UseSharedPeptidesForProteinQuant = f.UseSharedPeptidesForProteinQuant;
+            //IsoTracker = f.IsoTracker;
 
             RandomSeed = bayesianSettings.RandomSeed;
         }
@@ -153,7 +156,9 @@ public static FlashLfqEngine CreateEngineWithSettings(FlashLfqSettings settings,
                 mcmcBurninSteps: settings.McmcBurninSteps,
                 useSharedPeptidesForProteinQuant: settings.UseSharedPeptidesForProteinQuant,
                 randomSeed: settings.RandomSeed,
+                //isoTracker: settings.IsoTracker,
                 peptideSequencesToQuantify: peptidesForMbr
+                
                 );
         }
 
diff --git a/Util/Util.csproj b/Util/Util.csproj
index ce7e1f0..6fc12f7 100644
--- a/Util/Util.csproj
+++ b/Util/Util.csproj
@@ -13,7 +13,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.553" />
+    <PackageReference Include="mzLib" Version="8.0.0" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>