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 4.12.0

• 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