SpectronauttoMSstatsFormat: Generate MSstats required input format for Spectronaut output

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

Description

Convert Spectronaut output into the required input format for MSstats.

Usage

SpectronauttoMSstatsFormat(input,
      annotation = NULL,
      intensity = 'PeakArea',
      filter_with_Qvalue = TRUE,
      qvalue_cutoff = 0.01,
      useUniquePeptide = TRUE,
      fewMeasurements="remove",
      removeProtein_with1Feature = FALSE,
      summaryforMultipleRows=max)	

Arguments

input	name of Spectronaut output, which is long-format. ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity, F.ExcludedFromQuantification are required. Rows with F.ExcludedFromQuantification=True will be removed.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Spectronaut, use annotation=NULL (default). It will use the annotation information from input.
intensity	'PeakArea'(default) uses not normalized peak area. 'NormalizedPeakArea' uses peak area normalized by Spectronaut.
filter_with_Qvalue	TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in EG.Qvalue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.
qvalue_cutoff	Cutoff for EG.Qvalue. 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.
removeProtein_with1Feature	TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.

Value

data.frame with the required format of MSstats.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

Examples

# Please check section 5.2. 
# Suggested workflow with Spectronaut output for DIA in MSstats user manual.
# Output of SpectronauttoMSstatsFormat 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.