PDtoMSstatsFormat: Generate MSstats required input format for Proteome...

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

Description

Convert Proteome discoverer output into the required input format for MSstats.

Usage

PDtoMSstatsFormat(input,
      annotation,
      useNumProteinsColumn=FALSE,
      useUniquePeptide=TRUE,
      summaryforMultipleRows=max,
      fewMeasurements="remove",
      removeOxidationMpeptides=FALSE,
      removeProtein_with1Peptide=FALSE,
      which.quantification = 'Precursor.Area',
      which.proteinid = 'Protein.Group.Accessions',
      which.sequence = 'Sequence' )	

Arguments

input	name of Proteome discover PSM output, which is long-format. "Protein.Group.Accessions", "#Proteins", "Sequence", "Modifications", "Charge", "Intensity", "Spectrum.File" are required.
annotation	name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run information. 'Run' will be matched with 'Spectrum.File'.
useNumProteinsColumn	TRUE removes peptides which have more than 1 in # Proteins column of PD output.
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 multiple intensities.
fewMeasurements	'remove'(default) will remove the features that have 1 or 2 measurements across runs.
removeOxidationMpeptides	TRUE will remove the modified peptides including 'Oxidation (M)' in 'Modifications' column. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
which.quantification	Use 'Precursor.Area'(default) column for quantified intensities. 'Intensity' or 'Area' can be used instead.
which.proteinid	Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead.
which.sequence	Use 'Sequence'(default) column for peptide sequence. 'Annotated.Sequence' can be used instead.

Value

data.frame with the required format of MSstats.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

Examples

# Please check section 4.5. 
## Suggested workflow with Proteome Discoverer output for DDA in MSstats user manual.
# Output of PDtoMSstatsFormat 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.