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


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Documentation for package ‘MSstats’ version 2.6.0

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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