MSstats-package         Tools for protein significance analysis in
                        LC-MS,SRM and DIA for label-free or label-based
                        proteomic experiments
QuantData               Quantitative data after data pre-processing and
                        quality control of MS runs
RawData                 Example dataset from a label-based SRM
                        experiment of a time course yeast study
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
quantification          Protein sample quantification or group
                        quantification
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
