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Added isoTracker support to GUI/CMD #152

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2cbe739
Added isoTracker support to GUI/CMD
Alexander-Sol Mar 18, 2025
f949d4c
idk
Alexander-Sol Mar 20, 2025
2ba42f2
nuget update
Alexander-Sol Mar 27, 2025
fd1a540
FixedMergeConflicts
Alexander-Sol Mar 27, 2025
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2 changes: 1 addition & 1 deletion CMD/CMD.csproj
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Expand Up @@ -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" />
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2 changes: 1 addition & 1 deletion GUI/GUI.csproj
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Expand Up @@ -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" />
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30 changes: 18 additions & 12 deletions GUI/MainWindow.xaml
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Expand Up @@ -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"
Expand Down Expand Up @@ -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" />
Expand All @@ -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" />
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4 changes: 4 additions & 0 deletions GUI/MainWindow.xaml.cs
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Expand Up @@ -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;
Expand Down Expand Up @@ -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))
{
Expand Down Expand Up @@ -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;
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2 changes: 1 addition & 1 deletion Test/Test.csproj
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Expand Up @@ -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" />
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9 changes: 7 additions & 2 deletions Util/FlashLfqSettings.cs
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Expand Up @@ -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>());
Expand All @@ -120,6 +122,7 @@ public FlashLfqSettings()
McmcSteps = f.McmcSteps;
McmcBurninSteps = f.McmcBurninSteps;
UseSharedPeptidesForProteinQuant = f.UseSharedPeptidesForProteinQuant;
//IsoTracker = f.IsoTracker;

RandomSeed = bayesianSettings.RandomSeed;
}
Expand Down Expand Up @@ -153,7 +156,9 @@ public static FlashLfqEngine CreateEngineWithSettings(FlashLfqSettings settings,
mcmcBurninSteps: settings.McmcBurninSteps,
useSharedPeptidesForProteinQuant: settings.UseSharedPeptidesForProteinQuant,
randomSeed: settings.RandomSeed,
//isoTracker: settings.IsoTracker,
peptideSequencesToQuantify: peptidesForMbr

);
}

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2 changes: 1 addition & 1 deletion Util/Util.csproj
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Expand Up @@ -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>
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