MaxQtoMSstatsFormat: Generate MSstats required input format for MaxQuant output

Description Usage Arguments Value Warning Author(s) Examples

View source: R/MaxQtoMSstatsFormat.R

Description

Convert MaxQuant output into the required input format for MSstats.

Usage

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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 (mnchoi67@gmail.com)

Examples

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# 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.