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

## Documentation for package ‘MSstats’ version 4.12.1

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

## 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
DIANNtoMSstatsFormat | Import Diann files
DIARawData | Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.
DIAUmpiretoMSstatsFormat | Import DIA-Umpire files
extractSDRF | Extract experimental design from MSstats format into SDRF format
FragPipetoMSstatsFormat | Import FragPipe files
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
makePeptidesDictionary | Prepare a peptides dictionary for global standards normalization
MaxQtoMSstatsFormat | Import MaxQuant files
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
MSstatsSelectFeatures | Feature selection before feature-level data summarization
MSstatsSummarizationOutput | Post-processing output from MSstats summarization
MSstatsSummarize | Feature-level data 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
OpenMStoMSstatsFormat | Import OpenMS files
OpenSWATHtoMSstatsFormat | Import OpenSWATH files
PDtoMSstatsFormat | Import Proteome Discoverer files
ProgenesistoMSstatsFormat | Import Progenesis files
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
SkylinetoMSstatsFormat | Import Skyline files
SpectronauttoMSstatsFormat | Import Spectronaut files
SRMRawData | Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study
theme_msstats | Theme for MSstats plots