Five GROUND_TRUTH entries in config.R list source columns that do not match what the hand-written MSstatsConvert converters use. Found while defining the correctness metric in #6.
proteome_discoverer$Intensity: PDtoMSstatsFormat defaults which.quantification to Precursor.Area, not Intensityspectronaut$ProductCharge: clean_Spectronaut resolves F.Charge or F.FrgZspectronaut$PeptideSequence: PEP.StrippedSequence is never accepted as a fallbackmetamorpheus$PeptideSequence: Base Sequence is not in req_colsmetamorpheus$PrecursorCharge: Peak Charge is not in req_cols
The PD one matters most. Scoring Intensity as correct while the reference converter quantifies from Precursor.Area would make the downstream comparison in #8 differ for reasons unrelated to mapping quality.
Blocks #7 producing valid numbers.
Five
GROUND_TRUTHentries inconfig.Rlist source columns that do not match what the hand-written MSstatsConvert converters use. Found while defining the correctness metric in #6.proteome_discoverer$Intensity:PDtoMSstatsFormatdefaultswhich.quantificationtoPrecursor.Area, notIntensityspectronaut$ProductCharge:clean_SpectronautresolvesF.ChargeorF.FrgZspectronaut$PeptideSequence:PEP.StrippedSequenceis never accepted as a fallbackmetamorpheus$PeptideSequence:Base Sequenceis not inreq_colsmetamorpheus$PrecursorCharge:Peak Chargeis not inreq_colsThe PD one matters most. Scoring
Intensityas correct while the reference converter quantifies fromPrecursor.Areawould make the downstream comparison in #8 differ for reasons unrelated to mapping quality.Blocks #7 producing valid numbers.