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Added option to quantify ambiguous peptides #2277

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Added option to quantify ambiguous peptides #2277

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dd03456
1.0.2 final commit with mzLib 5.0.39
nbollis Apr 19, 2023
dbcdf3e
added new mzlib
nbollis Apr 21, 2023
6ee0e92
Updated to most recent mzlib 1.0.139
nbollis Apr 29, 2023
e0adadf
Merge branch 'master' into 102with539mzlib
nbollis Apr 29, 2023
0a3251c
Fixed a metadraw test
nbollis Apr 29, 2023
1f64e28
Added Readers to product.wxs
Alexander-Sol Apr 29, 2023
ed56f23
Added changes enabling ambiguouspeptideQuant
Alexander-Sol Apr 29, 2023
253e808
Merge branch 'master' into AmbiguousQuantOption2
nbollis May 24, 2023
879611d
Fixed merge conflicts
Alexander-Sol Jul 22, 2023
3629c95
minor
Alexander-Sol Jul 24, 2023
f7bf4a7
Finished, changed installer version
Alexander-Sol Jul 25, 2023
113286a
Added support for Peptide Retention Times
Alexander-Sol Jul 31, 2023
e01b2eb
Version to 1.1.0
Alexander-Sol Aug 1, 2023
5eb1899
MRCv1_1_2
Alexander-Sol Aug 2, 2023
1d4f5f8
MRC v12
Alexander-Sol Aug 15, 2023
0d11320
Merge remote-tracking branch 'upstream/master' into AmbiguousQuantOpt…
Alexander-Sol Aug 15, 2023
e7c180d
Added option for in-source-oxidation
Alexander-Sol Aug 15, 2023
e858611
MRC 122
Alexander-Sol Aug 16, 2023
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2 changes: 1 addition & 1 deletion MetaMorpheus/CMD/CMD.csproj
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Expand Up @@ -24,7 +24,7 @@
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.539" />
<PackageReference Include="mzLib" Version="5.0.542" />
<PackageReference Include="Nett" Version="0.15.0" />
</ItemGroup>

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2 changes: 1 addition & 1 deletion MetaMorpheus/EngineLayer/EngineLayer.csproj
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Expand Up @@ -21,7 +21,7 @@
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.539" />
<PackageReference Include="mzLib" Version="5.0.542" />
<PackageReference Include="NETStandard.Library" Version="2.0.3" />
<PackageReference Include="Nett" Version="0.15.0" />
<PackageReference Include="Newtonsoft.Json" Version="13.0.1" />
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3 changes: 3 additions & 0 deletions MetaMorpheus/EngineLayer/GlobalVariables.cs
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Expand Up @@ -337,6 +337,9 @@ private static void SetMetaMorpheusVersion()
}
MetaMorpheusVersion = MetaMorpheusVersion.Substring(0, foundIndexes.Last());
}

// Change this before release!!!
MetaMorpheusVersion = "Alpha - Multi-Run Consensus v1.2.2";
}

private static void SetUpDataDirectory()
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2 changes: 1 addition & 1 deletion MetaMorpheus/GUI/GUI.csproj
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Expand Up @@ -55,7 +55,7 @@
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.539" />
<PackageReference Include="mzLib" Version="5.0.542" />
<PackageReference Include="Nett" Version="0.15.0" />
<PackageReference Include="Newtonsoft.Json" Version="13.0.1" />
<PackageReference Include="OxyPlot.Core" Version="2.0.0" />
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4 changes: 2 additions & 2 deletions MetaMorpheus/GUI/Properties/AssemblyInfo.cs
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Expand Up @@ -47,5 +47,5 @@
// You can specify all the values or you can default the Build and Revision Numbers
// by using the '*' as shown below:
// [assembly: AssemblyVersion("1.0.*")]
[assembly: AssemblyVersion("1.0.0.0")]
[assembly: AssemblyFileVersion("1.0.0.0")]
[assembly: AssemblyVersion("1.1.2.0")]
[assembly: AssemblyFileVersion("1.1.2.0")]
51 changes: 51 additions & 0 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
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Expand Up @@ -527,6 +527,40 @@
<ToolTip Content="Use the 'Experimental Design' to normalize intensity values from FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</CheckBox>
<CheckBox x:Name="CheckBoxReportPeptideRt" Content="Report peptide retention times">
<CheckBox.IsEnabled>
<MultiBinding Converter="{StaticResource boolOrConverter}">
<Binding ElementName="CheckBoxLFQ" Path ="IsChecked"/>
<Binding ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
</MultiBinding>
</CheckBox.IsEnabled>
<CheckBox.Visibility>
<MultiBinding Converter="{StaticResource boolOr2VisConverter}">
<Binding ElementName="CheckBoxLFQ" Path ="IsChecked"/>
<Binding ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
</MultiBinding>
</CheckBox.Visibility>
<ToolTipService.ToolTip>
<ToolTip Content="Report the retention time of the chromatographic peak apex for each peptide in the AllQuantifiedPeptides.tsv file" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</CheckBox>
<CheckBox x:Name="CheckBoxReportInSourceOxidation" Content="Report in-source oxidation as distinct peptides">
<CheckBox.IsEnabled>
<MultiBinding Converter="{StaticResource boolOrConverter}">
<Binding ElementName="CheckBoxLFQ" Path ="IsChecked"/>
<Binding ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
</MultiBinding>
</CheckBox.IsEnabled>
<CheckBox.Visibility>
<MultiBinding Converter="{StaticResource boolOr2VisConverter}">
<Binding ElementName="CheckBoxLFQ" Path ="IsChecked"/>
<Binding ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
</MultiBinding>
</CheckBox.Visibility>
<ToolTipService.ToolTip>
<ToolTip Content="Labels oxidized peptides the co-elute with their unoxidized counterparts" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</CheckBox>

<!-- Multiplex Options -->
<StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="0" Grid.Row="0">
Expand All @@ -546,6 +580,23 @@
</ComboBox>
</StackPanel>

<CheckBox x:Name="CheckBoxQuantifyAmbiguousPeptides" Content="Quantify ambiguous peptides">
<CheckBox.IsEnabled>
<MultiBinding Converter="{StaticResource boolOrConverter}">
<Binding ElementName="CheckBoxLFQ" Path ="IsChecked"/>
<Binding ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
</MultiBinding>
</CheckBox.IsEnabled>
<CheckBox.Visibility>
<MultiBinding Converter="{StaticResource boolOr2VisConverter}">
<Binding ElementName="CheckBoxLFQ" Path ="IsChecked"/>
<Binding ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
</MultiBinding>
</CheckBox.Visibility>
<ToolTipService.ToolTip>
<ToolTip Content="Reports identical intensity values for all ambiguous peptides associated with a given chromatographic peak" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</CheckBox>
</StackPanel>
</GroupBox>

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8 changes: 8 additions & 0 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
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Expand Up @@ -189,6 +189,11 @@ private void UpdateFieldsFromTask(SearchTask task)
CheckBoxLFQ.IsChecked = task.SearchParameters.DoLabelFreeQuantification;
CheckBoxMultiplex.IsChecked = task.SearchParameters.DoMultiplexQuantification;
MultiplexComboBox.SelectedItem = task.SearchParameters.MultiplexModId ?? _defaultMultiplexType;
CheckBoxNoQuant.IsChecked = !task.SearchParameters.DoLabelFreeQuantification && !task.SearchParameters.DoMultiplexQuantification;
CheckBoxLFQ.IsChecked = task.SearchParameters.DoLabelFreeQuantification;
CheckBoxQuantifyAmbiguousPeptides.IsChecked = task.SearchParameters.QuantifyAmbiguousPeptides;
CheckBoxReportPeptideRt.IsChecked = task.SearchParameters.ReportQuantifiedPeptideRetentionTime;
CheckBoxReportInSourceOxidation.IsChecked = task.SearchParameters.ReportInSourceOxidation;
// If Spectral Recovery is enabled
if (task.SearchParameters.WriteSpectralLibrary & task.SearchParameters.MatchBetweenRuns)
{
Expand Down Expand Up @@ -630,6 +635,9 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
TheTask.SearchParameters.DoMultiplexQuantification = CheckBoxMultiplex.IsChecked.Value;
TheTask.SearchParameters.MultiplexModId = (string)MultiplexComboBox.SelectedItem;
TheTask.SearchParameters.Normalize = CheckBoxNormalize.IsChecked.Value;
TheTask.SearchParameters.QuantifyAmbiguousPeptides = CheckBoxQuantifyAmbiguousPeptides.IsChecked.Value;
TheTask.SearchParameters.ReportQuantifiedPeptideRetentionTime = CheckBoxReportPeptideRt.IsChecked.Value;
TheTask.SearchParameters.ReportInSourceOxidation = CheckBoxReportInSourceOxidation.IsChecked.Value;
TheTask.SearchParameters.MatchBetweenRuns = CheckBoxMatchBetweenRuns.IsChecked.Value;
TheTask.SearchParameters.ModPeptidesAreDifferent = ModPepsAreUnique.IsChecked.Value;
TheTask.SearchParameters.QuantifyPpmTol = double.Parse(PeakFindingToleranceTextBox.Text, CultureInfo.InvariantCulture);
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2 changes: 1 addition & 1 deletion MetaMorpheus/GuiFunctions/GuiFunctions.csproj
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Expand Up @@ -14,7 +14,7 @@

<ItemGroup>
<PackageReference Include="itext7" Version="7.1.13" />
<PackageReference Include="mzLib" Version="1.0.539" />
<PackageReference Include="mzLib" Version="5.0.542" />
<PackageReference Include="OxyPlot.Wpf" Version="2.0.0" />
<PackageReference Include="Svg" Version="3.4.3" />
</ItemGroup>
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4 changes: 2 additions & 2 deletions MetaMorpheus/MetaMorpheus.sln
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Expand Up @@ -34,8 +34,8 @@ Global
{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|Any CPU.Build.0 = Release|Any CPU
{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|Any CPU.Build.0 = Debug|Any CPU
{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|Any CPU.ActiveCfg = Release|Any CPU
{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|Any CPU.Build.0 = Release|Any CPU
{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|Any CPU.ActiveCfg = Debug|Any CPU
{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|Any CPU.Build.0 = Debug|Any CPU
{FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
{FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Debug|Any CPU.Build.0 = Debug|Any CPU
{FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Release|Any CPU.ActiveCfg = Release|Any CPU
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26 changes: 24 additions & 2 deletions MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs
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Expand Up @@ -584,14 +584,36 @@ private void QuantificationAnalysis()
allIdentifications: flashLFQIdentifications,
normalize: Parameters.SearchParameters.Normalize,
ppmTolerance: Parameters.SearchParameters.QuantifyPpmTol,
quantifyAmbiguousPeptides: Parameters.SearchParameters.QuantifyAmbiguousPeptides,
reportPeptideRetentionTimes: Parameters.SearchParameters.ReportQuantifiedPeptideRetentionTime,
reportInSourceOxidation: Parameters.SearchParameters.ReportInSourceOxidation,
matchBetweenRunsPpmTolerance: Parameters.SearchParameters.QuantifyPpmTol, // If these tolerances are not equivalent, then MBR will falsely classify peptides found in the initial search as MBR peaks
matchBetweenRuns: Parameters.SearchParameters.MatchBetweenRuns,
silent: true,
maxThreads: CommonParameters.MaxThreadsToUsePerFile);


if (flashLFQIdentifications.Any())
{
Parameters.FlashLfqResults = FlashLfqEngine.Run();
Parameters.FlashLfqResults = FlashLfqEngine.Run(out List<Exception> exceptions);
if(Parameters.SearchParameters.QuantifyAmbiguousPeptides)
{
var outputFile = Path.Combine(Parameters.OutputFolder, "QuantificationErrorList.txt");
using (StreamWriter writer = new StreamWriter(outputFile))
{
if (exceptions.IsNotNullOrEmpty())
{
foreach(Exception e in exceptions)
{
writer.WriteLine(e.ToString());
}
}
else
{
writer.WriteLine("No errors to report. Great job!");
}
}
}
}

// get protein intensity back from FlashLFQ
Expand Down Expand Up @@ -649,7 +671,7 @@ private void HistogramAnalysis()
/// included, with each ion being reported in a separate column.
/// </summary>
/// <param name="psms">PSMs to be written</param>
/// <param name="filePath">Full file path, up to and including the filename and extensioh. </param>
/// <param name="filePath">Full file path, up to and including the filename and extension. </param>
protected void WritePsmsToTsv(IEnumerable<PeptideSpectralMatch> psms, string filePath)
{
if (Parameters.SearchParameters.DoMultiplexQuantification &&
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5 changes: 5 additions & 0 deletions MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
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Expand Up @@ -17,6 +17,8 @@ public SearchParameters()
DoLabelFreeQuantification = true;
DoSpectralRecovery = false;
QuantifyPpmTol = 5;
QuantifyAmbiguousPeptides = false;
ReportQuantifiedPeptideRetentionTime = false;
SearchTarget = true;
DecoyType = DecoyType.Reverse;
DoHistogramAnalysis = false;
Expand Down Expand Up @@ -67,6 +69,9 @@ public SearchParameters()
public bool MatchBetweenRuns { get; set; }
public bool Normalize { get; set; }
public double QuantifyPpmTol { get; set; }
public bool QuantifyAmbiguousPeptides { get; set; }
public bool ReportQuantifiedPeptideRetentionTime { get; set; }
public bool ReportInSourceOxidation { get; set; }
public bool DoHistogramAnalysis { get; set; }
public bool SearchTarget { get; set; }
public DecoyType DecoyType { get; set; }
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2 changes: 1 addition & 1 deletion MetaMorpheus/TaskLayer/TaskLayer.csproj
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Expand Up @@ -21,7 +21,7 @@
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.539" />
<PackageReference Include="mzLib" Version="5.0.542" />
<PackageReference Include="NetSerializer" Version="4.1.1" />
<PackageReference Include="Nett" Version="0.15.0" />
</ItemGroup>
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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/Test.csproj
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Expand Up @@ -23,7 +23,7 @@
<PackageReference Include="Microsoft.ML" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="mzLib" Version="1.0.539" />
<PackageReference Include="mzLib" Version="5.0.542" />
<PackageReference Include="NUnit" Version="3.13.3" />
<PackageReference Include="NUnit3TestAdapter" Version="4.2.1" />
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.1.0" />
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