Package: MSstatsConvert 1.22.1

Anthony Wu

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

MSstatsConvert provides tools for importing reports of Mass Spectrometry data processing tools into R format suitable for statistical analysis using the MSstats and MSstatsTMT packages.

Authors:Mateusz Staniak [aut], Devon Kohler [aut], Anthony Wu [aut, cre], Meena Choi [aut], Ting Huang [aut], Olga Vitek [aut]

# Install 'MSstatsConvert' in R:

install.packages('MSstatsConvert', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:MSstatsConvert-1.23.6(bioc 3.24)MSstatsConvert-1.22.1(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

massspectrometry proteomics software dataimport qualitycontrol cpp

6.75 score 8 packages 43 scripts 1.2k downloads 28 exports 5 dependencies

Last updated from:fe449ec0a4 (on RELEASE_3_23). Checks:1 WARNING, 13 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	152
linux-devel-arm64	NOTE	165
linux-devel-x86_64	NOTE	188
source / vignettes	OK	192
linux-release-arm64	NOTE	147
linux-release-x86_64	NOTE	262
macos-release-arm64	NOTE	133
macos-release-x86_64	NOTE	531
macos-oldrel-arm64	NOTE	308
macos-oldrel-x86_64	NOTE	570
windows-devel-arm64	NOTE	238
windows-devel-x86_64	NOTE	158
windows-release-arm64	NOTE	206
windows-release-x86_64	NOTE	118
windows-oldrel-x86_64	NOTE	109
wasm-release	OK	98

Exports:CheckDataHealth DIANNtoMSstatsFormat DIAUmpiretoMSstatsFormat FragPipetoMSstatsFormat getDataType getInputFile MaxQtoMSstatsFormat MaxQtoMSstatsTMTFormat MetamorpheusToMSstatsFormat MSstatsAnomalyScores MSstatsBalancedDesign MSstatsClean MSstatsImport MSstatsLogsSettings MSstatsMakeAnnotation MSstatsPreprocess MSstatsSaveSessionInfo OpenMStoMSstatsFormat OpenMStoMSstatsTMTFormat OpenSWATHtoMSstatsFormat PDtoMSstatsFormat PDtoMSstatsTMTFormat PhilosophertoMSstatsTMTFormat ProgenesistoMSstatsFormat ProteinProspectortoMSstatsTMTFormat SkylinetoMSstatsFormat SpectroMinetoMSstatsTMTFormat SpectronauttoMSstatsFormat

Dependencies:backports checkmate data.table Rcpp stringi

Working with MSstatsConvert

Rendered frommsstats_data_format.Rmdusingknitr::rmarkdown

Last update: 2026-07-16
Started: 2020-10-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Clean raw Proteome Discoverer data	.cleanRawPD
Convert output of converters to data.frame	as.data.frame.MSstatsValidated
Convert output of converters to data.table	as.data.table.MSstatsValidated
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.	CheckDataHealth
Import Diann files	DIANNtoMSstatsFormat
Import DIA-Umpire files	DIAUmpiretoMSstatsFormat
Import FragPipe files	FragPipetoMSstatsFormat
Get one of files contained in an instance of 'MSstatsInputFiles' class.	getInputFile getInputFile,MSstatsInputFiles-method getInputFile,MSstatsPhilosopherFiles-method
Import MaxQuant files	MaxQtoMSstatsFormat
Generate MSstatsTMT required input format from MaxQuant output	MaxQtoMSstatsTMTFormat
Import Metamorpheus files	MetamorpheusToMSstatsFormat
Run Anomaly Model	MSstatsAnomalyScores
Creates balanced design by removing overlapping fractions and filling incomplete rows	MSstatsBalancedDesign
Clean files generated by a signal processing tools.	MSstatsClean MSstatsClean,MSstatsDIANNFiles-method MSstatsClean,MSstatsDIAUmpireFiles-method MSstatsClean,MSstatsMaxQuantFiles-method MSstatsClean,MSstatsMetamorpheusFiles-method MSstatsClean,MSstatsOpenMSFiles-method MSstatsClean,MSstatsOpenSWATHFiles-method MSstatsClean,MSstatsPhilosopherFiles-method MSstatsClean,MSstatsProgenesisFiles-method MSstatsClean,MSstatsProteinProspectorFiles-method MSstatsClean,MSstatsProteomeDiscovererFiles-method MSstatsClean,MSstatsSkylineFiles-method MSstatsClean,MSstatsSpectroMineFiles-method MSstatsClean,MSstatsSpectronautFiles-method
Import files from signal processing tools.	MSstatsImport
Set how MSstats will log information from data processing	MSstatsLogsSettings
Create annotation	MSstatsMakeAnnotation
Preprocess outputs from MS signal processing tools for analysis with MSstats	MSstatsPreprocess
Save session information	MSstatsSaveSessionInfo
Import OpenMS files	OpenMStoMSstatsFormat
Generate MSstatsTMT required input format for OpenMS output	OpenMStoMSstatsTMTFormat
Import OpenSWATH files	OpenSWATHtoMSstatsFormat
Import Proteome Discoverer files	PDtoMSstatsFormat
Convert Proteome Discoverer output to MSstatsTMT format.	PDtoMSstatsTMTFormat
Convert Philosopher (Fragpipe) output to MSstatsTMT format.	PhilosophertoMSstatsTMTFormat
Import Progenesis files	ProgenesistoMSstatsFormat
Generate MSstatsTMT required input format from Protein Prospector output	ProteinProspectortoMSstatsTMTFormat
Import Skyline files	SkylinetoMSstatsFormat
Import data from SpectroMine	SpectroMinetoMSstatsTMTFormat
Import Spectronaut files	SpectronauttoMSstatsFormat