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

Documentation for package ‘MSstats’ version 2.2.0

MSstats-package	Tools for protein significance analysis in DDA,SRM and DIA for label-free or label-based proteomic experiments
dataProcess	Data pre-processing and quality control of MS runs of raw data
dataProcessPlots	Visualization for explanatory data analysis
designSampleSize	Planning future experimental designs of label-free and label-based LC-MS, SRM, DIA experiments in sample size calculation
designSampleSizePlots	Visualization for sample size calculation
groupComparison	Finding differentially abundant proteins across conditions in LC-MS, SRM and DIA experiment
groupComparisonPlots	Visualization for model-based analysis and summarizing differentially abundant proteins
modelBasedQCPlots	Visualization for model-based quality control in fitting model
MSstats	Tools for protein significance analysis in DDA,SRM and DIA for label-free or label-based proteomic experiments
QuantData	Quantitative data after data pre-processing and quality control of MS runs
quantification	Protein sample quantification or group quantification
RawData	Example dataset from a label-based SRM experiment of a time course yeast study
testResultMultiComparisons	Significance testing result of a set of comparisons between two groups
testResultOneComparison	Significance testing result of one comparison between two groups
transformMSnSetToMSstats	Transforms a MSnSet class dataset into a required input for MSstats
transformMSstatsToMSnSet	Transformation input format for MSstats to MSnSet class