# Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

## Documentation for package ‘MSstatsConvert’ version 1.22.1

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

## Help Pages

.cleanRawPD | Clean raw Proteome Discoverer data
as.data.frame.MSstatsValidated | Convert output of converters to data.frame
as.data.table.MSstatsValidated | Convert output of converters to data.table
CheckDataHealth | Takes as input the output of the SpectronauttoMSstatsFormat function and calculates various quality metrics to assess the health of the data. Requires Anomaly Detection model to be fit.
DIANNtoMSstatsFormat | Import Diann files
DIAUmpiretoMSstatsFormat | Import DIA-Umpire files
FragPipetoMSstatsFormat | Import FragPipe files
getInputFile | Get one of files contained in an instance of 'MSstatsInputFiles' class.
getInputFile-method | Get one of files contained in an instance of 'MSstatsInputFiles' class.
MaxQtoMSstatsFormat | Import MaxQuant files
MaxQtoMSstatsTMTFormat | Generate MSstatsTMT required input format from MaxQuant output
MetamorpheusToMSstatsFormat | Import Metamorpheus files
MSstatsAnomalyScores | Run Anomaly Model
MSstatsBalancedDesign | Creates balanced design by removing overlapping fractions and filling incomplete rows
MSstatsClean | Clean files generated by a signal processing tools.
MSstatsClean-method | Clean files generated by a signal processing tools.
MSstatsImport | Import files from signal processing tools.
MSstatsLogsSettings | Set how MSstats will log information from data processing
MSstatsMakeAnnotation | Create annotation
MSstatsPreprocess | Preprocess outputs from MS signal processing tools for analysis with MSstats
MSstatsSaveSessionInfo | Save session information
OpenMStoMSstatsFormat | Import OpenMS files
OpenMStoMSstatsTMTFormat | Generate MSstatsTMT required input format for OpenMS output
OpenSWATHtoMSstatsFormat | Import OpenSWATH files
PDtoMSstatsFormat | Import Proteome Discoverer files
PDtoMSstatsTMTFormat | Convert Proteome Discoverer output to MSstatsTMT format.
PhilosophertoMSstatsTMTFormat | Convert Philosopher (Fragpipe) output to MSstatsTMT format.
ProgenesistoMSstatsFormat | Import Progenesis files
ProteinProspectortoMSstatsTMTFormat | Generate MSstatsTMT required input format from Protein Prospector output
SkylinetoMSstatsFormat | Import Skyline files
SpectroMinetoMSstatsTMTFormat | Import data from SpectroMine
SpectronauttoMSstatsFormat | Import Spectronaut files