From 6bcc3dc3d275ec49b9868fcc07b392373d896c11 Mon Sep 17 00:00:00 2001 From: Swaraj Patil Date: Sat, 19 Sep 2026 10:35:59 -0400 Subject: [PATCH] Fix GROUND_TRUTH mappings against converters: - Correct PD, Spectronaut, and MetaMorpheus columns - Remove unsupported fallback mappings --- R/config.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/R/config.R b/R/config.R index 9ff4f88..97a32ec 100755 --- a/R/config.R +++ b/R/config.R @@ -62,10 +62,10 @@ MSSTATS_FIELDS <- c( GROUND_TRUTH <- list( spectronaut = list( ProteinName = c("PG.ProteinGroups", "PG.ProteinAccessions"), - PeptideSequence = c("EG.ModifiedSequence", "PEP.StrippedSequence"), + PeptideSequence = "EG.ModifiedSequence", PrecursorCharge = "FG.Charge", FragmentIon = "F.FrgIon", - ProductCharge = "F.Charge", + ProductCharge = c("F.Charge", "F.FrgZ"), Run = "R.FileName", Intensity = c("F.PeakArea", "F.NormalizedPeakArea", "F.PeakHeight", "F.NormalizedPeakHeight"), @@ -78,13 +78,13 @@ GROUND_TRUTH <- list( FragmentIon = NULL, ProductCharge = NULL, Run = "Spectrum.File", - Intensity = "Intensity", + Intensity = c("Precursor.Area", "Intensity", "Area"), Qvalue = NULL ), metamorpheus = list( ProteinName = "Protein Group", - PeptideSequence = c("Full Sequence", "Base Sequence"), - PrecursorCharge = c("Precursor Charge", "Peak Charge"), + PeptideSequence = "Full Sequence", + PrecursorCharge = "Precursor Charge", FragmentIon = NULL, ProductCharge = NULL, Run = "File Name",