transformMSnSetToMSstats: Transforms a MSnSet class dataset into a required input for...

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

Description

Convert MSnSet class into the required input format for MSstats

Usage

transformMSnSetToMSstats(ProteinName,PeptideSequence, PrecursorCharge, FragmentIon, 
  ProductCharge,IsotopeLabelType, Bioreplicate,Run, Condition, data)	

Arguments

data	name of dataset with MSnSet class
ProteinName	name of column in the MSnSet that contains protein information. If not assigned, "ProteinAccession" column will be used.
PeptideSequence	name of column in the MSnSet that contains information of peptide sequence. If not assigned, "PeptideSequence" column will be used.
PrecursorCharge	name of column in the MSnSet that contains information of peptide charge. If not assigned, "charge" will be used.
FragmentIon	name of column in the MSnSet that contains information of transition. If not assigned, value of "NA" will be used.
ProductCharge	name of column in the MSnSet that contains information of transition charge. If not assigned, value of "NA" will be used.
IsotopeLabelType	name of the column in phenoData component of MSnSet that contains labeling information. If not assigned, "mz" column will be used.
Bioreplicate	name of the column in phenoData component of MSnSet that contains unique ids of biological replicates of the corresponding samples. If not assigned, rownames of pData(data) will be used.
Run	name of the column in MSnSet that contains information of experimental MS runs. If not assigned, "file" column will be used.
Condition	names of the columns in phenoData that correspond to the group variables of interest. If more than one variable is listed, a concatentated variable is created based on the variables.

Details

raw : See MSnSet for the general format on the proteomics. Condition must be specified. Intensity should not be specified, as this information is extracted automatically from the assayData component of the MSnSet.

Warning

The types of experiment that MSstats can analyze are LC-MS, SRM, DIA(SWATH) with label-free or labeled synthetic peptides. MSstats does not support for metabolic labeling or iTRAQ experiments.

Author(s)

Ching-Yun Chang, Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

References

Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy, Trevor Killeen, Brendan MacLean and Olga Vitek. "MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments" Bioinformatics, 30(17):2524-2526, 2014.

Ching-Yun Chang, Paola Picotti, Ruth Huttenhain, Viola Heinzelmann-Schwarz, Marko Jovanovic, Ruedi Aebersold, Olga Vitek. "Protein significance analysis in selected reaction monitoring (SRM) measurements." Molecular & Cellular Proteomics, 11:M111.014662, 2012.

Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek. "Statistical protein quantification and significance analysis in label-free LC-M experiments with complex designs" BMC Bioinformatics, 13:S16, 2012.

Gatto, L. and Lilly, K.S. (2012). MSnbase-an R Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics, 28, 288-289.

Examples

	
library("MSnbase")
data(itraqdata)
class(itraqdata)

msnset <- quantify(itraqdata[10:15], method = "trap", reporters = iTRAQ4, verbose = FALSE)
msnset

pData(msnset)$group<-c("control","disease","control","disease")

transformMSnSetToMSstats(data=msnset,Condition="group")

lindsaypino/MSstats-patch documentation built on May 24, 2019, 6 p.m.