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

## Documentation for package ‘MSstats’ version 2.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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