parseMaxQuantMSMS: Parse MaxQuant msms.txt

In eahrne/SpectroX: Proteotypic peptide selection and SRM/PRM/HRM panel creation

Description

Parse MaxQuant msms.txt

Usage

parseMaxQuantMSMS(file, pepCutoff = 0.05, targetPeptides = NA,
  targetProteins = NA, filterContaminants = T,
  contaminantRegExp = "^CON_", selectedPTMRegExp = NA,
  filterNonExclusivePeptides = T, pepLength = c(1, Inf),
  chargeState = c(1, Inf), label = NA, maxMissedCleavages = 0,
  keepBestSpectrumOnly = T, requiredPepSeqRegExp = ".", ...)

Arguments

file	path
pepCutoff	numeric default 0.05
targetPeptides	character default NA
targetProteins	character default NA
filterContaminants	TRUE
contaminantRegExp	'^CON_'
selectedPTMRegExp	NA
filterNonExclusivePeptides	default TRUE
pepLength	default [1,Inf)
chargeState	default [1,Inf)
label	(Arg10 and Lys8 only filter) options NA (deafault,no filter), 'light','heavy'
keepBestSpectrumOnly	keep top-scoring spectrum only, per peptidoform, default TRUE
requiredSequenceRegExp	dafualt '.' (no filter)

Details

No details

Value

data.frame of maxQuant psm level results

Note

No note

References

NA

Examples

print("No examples")

eahrne/SpectroX documentation built on May 21, 2019, 3:09 a.m.