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Made updates pertaining to PIP-ECHO #2468

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273b1a6
Made updates pertaining to PIP-ECHO
Alexander-Sol Feb 8, 2025
ed67fb8
Addressed nic's comments
Alexander-Sol Feb 11, 2025
a92f30f
Simplified SearchTaskWindow xaml
Alexander-Sol Feb 11, 2025
e8d0c27
Updated tool tip output
Alexander-Sol Feb 11, 2025
5ff997e
Updated MBR Q-Value label
Alexander-Sol Feb 11, 2025
46ed0aa
Merge branch 'master' into quantGUIUpdate
nbollis Feb 12, 2025
2e2cf5d
Update GlobalGuiSettings.cs
Alexander-Sol Feb 12, 2025
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2 changes: 1 addition & 1 deletion MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -198,7 +198,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)

if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
MaxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, fieldNotUsed, MaxModsPerPeptideTextBox.Text, fieldNotUsed,
fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, fieldNotUsed, MaxModsPerPeptideTextBox.Text, fieldNotUsed,
null, null, null))
{
return;
Expand Down
2 changes: 1 addition & 1 deletion MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
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Expand Up @@ -359,7 +359,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)

if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
MaxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState.ToString(), NumberOfPeaksToKeepPerWindowTextBox.Text, MinimumAllowedIntensityRatioToBasePeakTexBox.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState.ToString(), NumberOfPeaksToKeepPerWindowTextBox.Text, MinimumAllowedIntensityRatioToBasePeakTexBox.Text,
null, null, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, null))
{
return;
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2 changes: 1 addition & 1 deletion MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
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Expand Up @@ -247,7 +247,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)

if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecusorMsTlTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState.ToString(), TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text, TxtBoxMaxModPerPep.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState.ToString(), TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text, TxtBoxMaxModPerPep.Text,
fieldNotUsed, null, null, null))
{
return;
Expand Down
27 changes: 24 additions & 3 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
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Expand Up @@ -428,10 +428,10 @@
<ToolTip Content="Intensity of reporter ions are reported as additional columns in AllPeptides.psmtsv and AllPSMs.psmtsv" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"/>
</ToolTipService.ToolTip>
</RadioButton>
<RadioButton x:Name="CheckBoxLFQwSpectralRecovery" Content="LFQ + Spectral Recovery: Spectral recovery finds misidentified MS/MS spectra common in single-cell proteomics data"
<RadioButton x:Name="CheckBoxLFQwSpectralRecovery" Content="LFQ + Spectral Recovery: Spectral recovery finds missed MS/MS spectra common in single-cell proteomics data"
GroupName="QuantType" Click="SpectralRecoveryUpdate">
<ToolTipService.ToolTip>
<ToolTip Content="Match between runs analysis via spectral library search" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
<ToolTip Content="Re-analyzes MS/MS spectra based on the results of MBR to find spectra that may have been missed during the inital search" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</RadioButton>

Expand Down Expand Up @@ -508,7 +508,7 @@
</MultiBinding>
</CheckBox.Visibility>
<ToolTipService.ToolTip>
<ToolTip Content="(LFQ) Use MS2 identifications from one run to quantify those same peptides in other runs where they were not identified&#x0a;Selecting &quot;Write Spectral Library&quot; in the Output Options below will enable additional MBR analysis" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
<ToolTip Content="(LFQ) Use MS2 identifications from one run to quantify those same peptides in other runs where they were not identified" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</CheckBox>
<CheckBox x:Name="CheckBoxNormalize" Content="Normalize quantification results">
Expand Down Expand Up @@ -545,6 +545,27 @@
<ToolTip Content="Use peptide sequences shared between proteins for protein quantification" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</CheckBox>
<StackPanel Orientation="Horizontal">
<StackPanel.IsEnabled>
<MultiBinding Converter="{StaticResource boolOrConverter}">
<Binding ElementName="CheckBoxLFQ" Path ="IsChecked"/>
<Binding ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
</MultiBinding>
</StackPanel.IsEnabled>
<StackPanel.Visibility>
<MultiBinding Converter="{StaticResource boolOr2VisConverter}">
<Binding ElementName="CheckBoxLFQ" Path ="IsChecked"/>
<Binding ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
</MultiBinding>
</StackPanel.Visibility>

<local:DoubleTextBoxControl x:Name="MbrFdrThresholdTextBox" Width="45" Height="20">
<ToolTipService.ToolTip>
<ToolTip Content="Q-Value Threshold for MBR&#x0a;Determines which MBR matches will be reported in the AllQuantifiedPeptides and AllQuantifiedProteinGroups outputs" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</local:DoubleTextBoxControl>
<Label x:Name="MbrFdrThreshold" Content=" MBR Q-Value Threshold" />
</StackPanel>

<!-- Multiplex Options -->
<StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="0" Grid.Row="0">
Expand Down
3 changes: 3 additions & 0 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
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Expand Up @@ -261,6 +261,7 @@ private void UpdateFieldsFromTask(SearchTask task)
CheckBoxQuantifyUnlabeledForSilac.IsChecked = task.CommonParameters.DigestionParams.GeneratehUnlabeledProteinsForSilac;
PeakFindingToleranceTextBox.Text = task.SearchParameters.QuantifyPpmTol.ToString(CultureInfo.InvariantCulture);
CheckBoxMatchBetweenRuns.IsChecked = task.SearchParameters.MatchBetweenRuns;
MbrFdrThresholdTextBox.Text = task.SearchParameters.MbrFdrThreshold.ToString(CultureInfo.InvariantCulture);
CheckBoxNormalize.IsChecked = task.SearchParameters.Normalize;
ModPepsAreUnique.IsChecked = task.SearchParameters.ModPeptidesAreDifferent;
CheckBoxHistogramAnalysis.IsChecked = task.SearchParameters.DoHistogramAnalysis;
Expand Down Expand Up @@ -441,6 +442,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
MaxThreadsTextBox.Text,
MinScoreAllowed.Text,
PeakFindingToleranceTextBox.Text,
MbrFdrThresholdTextBox.Text,
HistogramBinWidthTextBox.Text,
DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState.ToString(),
NumberOfPeaksToKeepPerWindowTextBox.Text,
Expand Down Expand Up @@ -640,6 +642,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
TheTask.SearchParameters.MultiplexModId = (string)MultiplexComboBox.SelectedItem;
TheTask.SearchParameters.Normalize = CheckBoxNormalize.IsChecked.Value;
TheTask.SearchParameters.MatchBetweenRuns = CheckBoxMatchBetweenRuns.IsChecked.Value;
TheTask.SearchParameters.MbrFdrThreshold = double.Parse(MbrFdrThresholdTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.ModPeptidesAreDifferent = ModPepsAreUnique.IsChecked.Value;
TheTask.SearchParameters.QuantifyPpmTol = double.Parse(PeakFindingToleranceTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.SearchTarget = CheckBoxTarget.IsChecked.Value;
Expand Down
2 changes: 1 addition & 1 deletion MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -239,7 +239,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)

if (!GlobalGuiSettings.CheckTaskSettingsValidity(XLPrecusorMsTlTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState.ToString(), TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState.ToString(), TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text,
fieldNotUsed, fieldNotUsed, null, null, null))
{
return;
Expand Down
15 changes: 14 additions & 1 deletion MetaMorpheus/GUI/Util/GlobalGuiSettings.cs
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Expand Up @@ -23,6 +23,7 @@ public static bool CheckTaskSettingsValidity(string precursorMassTolerance,
string maxThreads,
string minScore,
string peakFindingTolerance,
string mbrFdrThreshold,
string histogramBinWidth,
string deconMaxAssumedCharge,
string numberOfPeaksToKeepPerWindow,
Expand Down Expand Up @@ -50,6 +51,7 @@ string minInternalIonLength
(CheckMaxThreads(maxThreads)),
(CheckMinScoreAllowed(minScore)),
(CheckPeakFindingTolerance(peakFindingTolerance)),
(CheckMbrFdrThreshold(mbrFdrThreshold)),
(CheckHistogramBinWidth(histogramBinWidth)),
(CheckDeconvolutionMaxAssumedChargeState(deconMaxAssumedCharge)),
(CheckTopNPeaks(numberOfPeaksToKeepPerWindow)),
Expand Down Expand Up @@ -271,7 +273,18 @@ public static bool CheckPeakFindingTolerance(string text)
}
return true;
}


public static bool CheckMbrFdrThreshold(string text)
{
if (!double.TryParse(text, NumberStyles.Any, CultureInfo.InvariantCulture, out double mbrFdrThreshold) || mbrFdrThreshold > 1)
{
MessageBox.Show("The MBR FDR Threshold is invalid. \n You entered " + '"' + text + '"' + "\n Please enter a positive number less than or equal to 1.");
return false;
}
return true;
}


public static bool CheckHistogramBinWidth(string text)
{
if (!double.TryParse(text, NumberStyles.Any, CultureInfo.InvariantCulture, out double binWidth) || binWidth < 0 || binWidth > 1)
Expand Down
25 changes: 15 additions & 10 deletions MetaMorpheus/TaskLayer/FilteredPsms.cs
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Expand Up @@ -162,18 +162,23 @@ public static IEnumerable<SpectralMatch> FilterByQValue(this IEnumerable<Spectra
{
yield return psm;
}
else if (filterType == FilterType.PepQValue)
else if (psm.GetFdrInfo(filterAtPeptideLevel) != null)
{
if (psm.GetFdrInfo(filterAtPeptideLevel).PEP_QValue <= qValueThreshold)
switch(filterType)
{
yield return psm;
}
}
else
{
if (psm.GetFdrInfo(filterAtPeptideLevel).QValue <= qValueThreshold && psm.GetFdrInfo(filterAtPeptideLevel).QValueNotch <= qValueThreshold)
{
yield return psm;
case FilterType.PepQValue:
if (psm.GetFdrInfo(filterAtPeptideLevel).PEP_QValue <= qValueThreshold)
{
yield return psm;
}
break;
case FilterType.QValue:
default:
if (psm.GetFdrInfo(filterAtPeptideLevel).QValue <= qValueThreshold && psm.GetFdrInfo(filterAtPeptideLevel).QValueNotch <= qValueThreshold)
{
yield return psm;
}
break;
}
}
}
Expand Down
30 changes: 26 additions & 4 deletions MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs
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Expand Up @@ -288,12 +288,22 @@ private void QuantificationAnalysis()
// get PSMs to pass to FlashLFQ
var psmsForQuantification = FilteredPsms.Filter(Parameters.AllPsms,
CommonParameters,
includeDecoys: false,
includeDecoys: Parameters.SearchParameters.MatchBetweenRuns, // Decoys are required for PIP-ECHO, but are not written to the output file
includeContaminants: true,
includeAmbiguous: false,
includeAmbiguousMods: false,
includeHighQValuePsms: false);

// Only these peptides will be written to the AllQuantifiedPeptides.tsv output file
var peptideSequencesForQuantification = FilteredPsms.Filter(Parameters.AllPsms,
CommonParameters,
includeDecoys: false,
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includeContaminants: true,
includeAmbiguous: false,
includeAmbiguousMods: false,
includeHighQValuePsms: false,
filterAtPeptideLevel: true).Select(p => p.FullSequence).ToList();

// pass protein group info for each PSM
var psmToProteinGroups = new Dictionary<SpectralMatch, List<FlashLFQ.ProteinGroup>>();
if (ProteinGroups != null && ProteinGroups.Count != 0) //ProteinGroups can be null if parsimony wasn't done, and it can be empty if you're doing the two peptide rule
Expand Down Expand Up @@ -501,12 +511,22 @@ private void QuantificationAnalysis()
var flashLFQIdentifications = new List<Identification>();
foreach (var spectraFile in psmsGroupedByFile)
{
var rawfileinfo = spectraFileInfo.Where(p => p.FullFilePathWithExtension.Equals(spectraFile.Key)).First();
var rawfileinfo = spectraFileInfo.First(p => p.FullFilePathWithExtension.Equals(spectraFile.Key));

foreach (var psm in spectraFile)
{
flashLFQIdentifications.Add(new Identification(rawfileinfo, psm.BaseSequence, psm.FullSequence,
psm.BioPolymerWithSetModsMonoisotopicMass.Value, psm.ScanRetentionTime, psm.ScanPrecursorCharge, psmToProteinGroups[psm]));
flashLFQIdentifications.Add(
new Identification(
fileInfo: rawfileinfo,
psm.BaseSequence,
psm.FullSequence,
psm.BioPolymerWithSetModsMonoisotopicMass.Value,
psm.ScanRetentionTime,
psm.ScanPrecursorCharge,
psmToProteinGroups[psm],
psmScore: psm.Score,
qValue: psmsForQuantification.FilterType == FilterType.QValue ? psm.FdrInfo.QValue : psm.FdrInfo.PEP_QValue,
decoy: psm.IsDecoy));
}
}

Expand All @@ -517,7 +537,9 @@ private void QuantificationAnalysis()
ppmTolerance: Parameters.SearchParameters.QuantifyPpmTol,
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,
matchBetweenRunsFdrThreshold: Parameters.SearchParameters.MbrFdrThreshold,
useSharedPeptidesForProteinQuant: Parameters.SearchParameters.UseSharedPeptidesForLFQ,
peptideSequencesToQuantify: Parameters.SearchParameters.SilacLabels == null ? peptideSequencesForQuantification : null, // Silac is doing it's own thing, no need to pass in peptide sequences
silent: true,
maxThreads: CommonParameters.MaxThreadsToUsePerFile);

Expand Down
2 changes: 2 additions & 0 deletions MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
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Expand Up @@ -18,6 +18,7 @@ public SearchParameters()
UseSharedPeptidesForLFQ = false;
DoSpectralRecovery = false;
QuantifyPpmTol = 5;
MbrFdrThreshold = 0.01;
SearchTarget = true;
DecoyType = DecoyType.Reverse;
DoHistogramAnalysis = false;
Expand Down Expand Up @@ -67,6 +68,7 @@ public SearchParameters()
public bool ModPeptidesAreDifferent { get; set; }
public bool NoOneHitWonders { get; set; }
public bool MatchBetweenRuns { get; set; }
public double MbrFdrThreshold { get; set; }
public bool Normalize { get; set; }
public double QuantifyPpmTol { get; set; }
public bool DoHistogramAnalysis { get; set; }
Expand Down
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