MaxQtoMSstatsFormat: Generate MSstats required input format for MaxQuant output

In MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Description

Convert MaxQuant output into the required input format for MSstats.

Usage

MaxQtoMSstatsFormat(evidence, 
      annotation,
      proteinGroups,
      proteinID="Proteins", 
      useUniquePeptide=TRUE, 
      summaryforMultipleRows=max, 
      fewMeasurements="remove", 
      removeMpeptides=FALSE,
      removeOxidationMpeptides=FALSE,
      removeProtein_with1Peptide=FALSE)	

Arguments

evidence	name of 'evidence.txt' data, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Raw.file, Condition, BioReplicate, Run, IsotopeLabelType information.
proteinGroups	name of 'proteinGroups.txt' data. It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'.
proteinID	'Proteins'(default) or 'Leading.razor.protein' for Protein ID.
useUniquePeptide	TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of all.
fewMeasurements	'remove'(default) will remove the features that have 1 or 2 measurements across runs. 'keep' will keep all features.
removeMpeptides	TRUE will remove the peptides including 'M' sequence. FALSE is default.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.

Value

data.frame with the required format of MSstats.

Warning

MSstats does not support for metabolic labeling or iTRAQ experiments.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

Examples

# Please check section 4.3. Suggested workflow with MaxQuant output for DDA in MSstats user manual.
# Output of MaxQtoMSstatsFormat function should have the same 10 columns as an example dataset.

head(DDARawData)

Example output

  ProteinName PeptideSequence PrecursorCharge FragmentIon ProductCharge
1      bovine     S.PVDIDTK_5               5          NA            NA
2      bovine     S.PVDIDTK_5               5          NA            NA
3      bovine     S.PVDIDTK_5               5          NA            NA
4      bovine     S.PVDIDTK_5               5          NA            NA
5      bovine     S.PVDIDTK_5               5          NA            NA
6      bovine     S.PVDIDTK_5               5          NA            NA
  IsotopeLabelType Condition BioReplicate Run Intensity
1                L        C1            1   1   2636792
2                L        C1            1   2   1992418
3                L        C1            1   3   1982146
4                L        C2            1   4   5019594
5                L        C2            1   5   4560468
6                L        C2            1   6   3627849

MSstats documentation built on Feb. 28, 2021, 2:01 a.m.