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[WIP] filter psms for flashlfq only by qvalue and qvalue notch #2259

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[WIP] filter psms for flashlfq only by qvalue and qvalue notch #2259

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14 changes: 2 additions & 12 deletions TaskLayer/SearchTask/PostSearchAnalysisTask.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -254,21 +254,11 @@ private void QuantificationAnalysis()
}

// get PSMs to pass to FlashLFQ
List<PeptideSpectralMatch> unambiguousPsmsBelowOnePercentFdr = new();
if (Parameters.AllPsms.Count > 100)//PEP is not computed when there are fewer than 100 psms
{
unambiguousPsmsBelowOnePercentFdr = Parameters.AllPsms.Where(p =>
p.FdrInfo.PEP_QValue <= 0.01
&& !p.IsDecoy
&& p.FullSequence != null).ToList(); //if ambiguous, there's no full sequence
}
else
{
unambiguousPsmsBelowOnePercentFdr = Parameters.AllPsms.Where(p =>
List<PeptideSpectralMatch> unambiguousPsmsBelowOnePercentFdr = Parameters.AllPsms.Where(p =>
p.FdrInfo.QValue <= 0.01
&& p.FdrInfo.QValueNotch <= 0.01
&& !p.IsDecoy
&& p.FullSequence != null).ToList(); //if ambiguous, there's no full sequence
}

// pass protein group info for each PSM
var psmToProteinGroups = new Dictionary<PeptideSpectralMatch, List<FlashLFQ.ProteinGroup>>();
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