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

## Documentation for package ‘MSstats’ version 4.19.3

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

## Help Pages

checkRepeatedDesign | Check if data represents repeated measurements design
dataProcess | Process MS data: clean, normalize and summarize before differential analysis
dataProcessPlots | Visualization for explanatory data analysis
DDARawData | Example dataset from a label-free DDA, a controlled spike-in experiment.
DDARawData.Skyline | Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.
designSampleSize | Planning future experimental designs of Selected Reaction Monitoring (SRM), Data-Dependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA or SWATH-MS) experiments in sample size calculation
designSampleSizePlots | Visualization for sample size calculation
DIARawData | Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.
example_SDRF | Example SDRF.
extractSDRF | Extract experimental design from MSstats format into SDRF format
getProcessed | Get feature-level data to be used in the MSstatsSummarizationOutput function
getSamplesInfo | Get information about number of measurements for each group
getSelectedProteins | Get proteins based on names or integer IDs
groupComparison | Whole plot testing
groupComparisonPlots | Visualization for model-based analysis and summarizing differentially abundant proteins
groupComparisonQCPlots | Visualization for model-based quality control in fitting model
makePeptidesDictionary | Prepare a peptides dictionary for global standards normalization
modelBasedQCPlots | Visualization for model-based quality control in fitting model
MSstatsContrastMatrix | Create a contrast matrix for groupComparison function
MSstatsGroupComparison | Group comparison
MSstatsGroupComparisonOutput | Create output of group comparison based on results for individual proteins
MSstatsGroupComparisonSingleProtein | Group comparison for a single protein
MSstatsHandleMissing | Handle censored missing values
MSstatsMergeFractions | Re-format the data before feature selection
MSstatsNormalize | Normalize MS data
MSstatsPrepareForDataProcess | Prepare data for processing by 'dataProcess' function
MSstatsPrepareForGroupComparison | Prepare output for dataProcess for group comparison
MSstatsPrepareForSummarization | Prepare feature-level data for protein-level summarization
MSstatsQualityMetricsPlot | Plot quality metrics from converter output
MSstatsSelectFeatures | Feature selection before feature-level data summarization
MSstatsSummarizationOutput | Post-processing output from MSstats summarization
MSstatsSummarizeSingleLinear | Linear model-based summarization for a single protein
MSstatsSummarizeSingleTMP | Tukey Median Polish summarization for a single protein
MSstatsSummarizeWithMultipleCores | Feature-level data summarization with multiple cores
MSstatsSummarizeWithSingleCore | Feature-level data summarization with 1 core
quantification | Protein sample quantification or group quantification
savePlot | Save a plot to pdf file
SDRFtoAnnotation | Convert SDRF experimental design file into an MSstats annotation file
SRMRawData | Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study
theme_msstats | Theme for MSstats plots
validateAnnotation | Check if annotation matches intended experimental design