SkylinetoMSstatsFormat: Generate MSstats required input format for Skyline output

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

Description

Preprocess MSstats input report from Skyline and convert into the required input format for MSstats.

Usage

SkylinetoMSstatsFormat(input,
      annotation = NULL,
      removeiRT = TRUE,
      filter_with_Qvalue = TRUE,
      qvalue_cutoff = 0.01,
      useUniquePeptide = TRUE,
      fewMeasurements="remove",
      removeOxidationMpeptides = FALSE,
      removeProtein_with1Feature = FALSE)	

Arguments

input	name of MSstats input report from Skyline, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Skyline, use annotation=NULL (default). It will use the annotation information from input.
removeiRT	TRUE(default) will remove the proteins or peptides which are labeld 'iRT' in 'StandardType' column. FALSE will keep them.
filter_with_Qvalue	TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in DetectionQValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.
qvalue_cutoff	Cutoff for DetectionQValue. default is 0.01.
useUniquePeptide	TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
fewMeasurements	'remove' (default) will remove the features that have 1 or 2 measurements across runs.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Feature	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.

Value

data.frame with the required format of MSstats.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

Examples

# Please check section 4.2. Suggested workflow with Skyline output for DDA in MSstats user manual.
# Output of SkylinetoMSstatsFormat 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.