FlashLFQ now enables selection of peptides to be quantified #779
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…ides will be quantified/reported
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #779 +/- ##
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+ Coverage 75.23% 75.25% +0.02%
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Files 195 195
Lines 30455 30484 +29
Branches 3053 3058 +5
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+ Hits 22913 22942 +29
Misses 7027 7027
Partials 515 515
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trishorts
requested review from
trishorts,
YulingDai,
elaboy,
nbollis,
zhuoxinshi and
RayMSMS
trishorts
reviewed
May 20, 2024
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| public FlashLfqResults(List<SpectraFileInfo> spectraFiles, List<Identification> identifications) | ||
| public FlashLfqResults(List<SpectraFileInfo> spectraFiles, List<Identification> identifications, HashSet<string> peptides = null) |
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should peptides be peptideFullSequencesToQuantify?
trishorts
reviewed
May 20, 2024
mzLib/FlashLFQ/FlashLFQResults.cs
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| foreach (SpectraFileInfo file in spectraFiles) | ||
| { | ||
| Peaks.Add(file, new List<ChromatographicPeak>()); | ||
| } | ||
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| foreach (Identification id in identifications) | ||
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| // Only quantify peptides within the set of valid peptide sequences. This is done to enable pepitde-level FDR control of reported results |
trishorts
reviewed
May 20, 2024
mzLib/FlashLFQ/FlashLfqEngine.cs
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| /// Other peptides may appear in the QuantifiedPeaks output, but this list is used to enable | ||
| /// peptide-level FDR filtering | ||
| /// </summary> | ||
| public HashSet<string> PeptidesToQuantify { get; init; } |
trishorts
reviewed
May 20, 2024
| @@ -479,19 +480,29 @@ public static void TestFlashLfqMergeResults() | |||
| public static void TestFlashLfqMatchBetweenRuns() | |||
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can you add a comment for this test
nbollis
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May 20, 2024
trishorts
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nbollis
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elaboy
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Previously, flashLFQ would report peptides that had a peptide level FDR greater than 1%. This is because FlashLFQ usually only considers PSMs for input (and therefore, PSM level FDR).
I added an optional parameter to FlashLFQ engine that allows users to pass in a list of strings representing that peptides that should be quantified/used to calculate protein intensities.