Package: MSstatsConvert 1.22.0

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]

MSstatsConvert_1.22.0.tar.gz
MSstatsConvert_1.22.0.zip(r-4.7)MSstatsConvert_1.22.0.zip(r-4.6)MSstatsConvert_1.22.0.zip(r-4.5)
MSstatsConvert_1.22.0.tgz(r-4.6-x86_64)MSstatsConvert_1.22.0.tgz(r-4.6-arm64)MSstatsConvert_1.22.0.tgz(r-4.5-x86_64)MSstatsConvert_1.22.0.tgz(r-4.5-arm64)
MSstatsConvert_1.22.0.tar.gz(r-4.7-arm64)MSstatsConvert_1.22.0.tar.gz(r-4.7-x86_64)MSstatsConvert_1.22.0.tar.gz(r-4.6-arm64)MSstatsConvert_1.22.0.tar.gz(r-4.6-x86_64)
MSstatsConvert_1.22.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MSstatsConvert/json (API)
NEWS

# 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-1.23.0(bioc 3.24)MSstatsConvert-1.22.0(bioc 3.23)

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

massspectrometryproteomicssoftwaredataimportqualitycontrolcpp

6.57 score 8 packages 28 scripts 1.0k downloads 28 exports 6 dependencies

Last updated from:074a559338 (on RELEASE_3_23). Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING207
linux-devel-arm64NOTE185
linux-devel-x86_64NOTE313
source / vignettesOK256
linux-release-arm64NOTE217
linux-release-x86_64NOTE196
macos-release-arm64NOTE165
macos-release-x86_64NOTE256
macos-oldrel-arm64NOTE137
macos-oldrel-x86_64NOTE207
windows-develNOTE132
windows-releaseNOTE128
windows-oldrelNOTE125
wasm-releaseOK164

Exports:CheckDataHealthDIANNtoMSstatsFormatDIAUmpiretoMSstatsFormatFragPipetoMSstatsFormatgetDataTypegetInputFileMaxQtoMSstatsFormatMaxQtoMSstatsTMTFormatMetamorpheusToMSstatsFormatMSstatsAnomalyScoresMSstatsBalancedDesignMSstatsCleanMSstatsImportMSstatsLogsSettingsMSstatsMakeAnnotationMSstatsPreprocessMSstatsSaveSessionInfoOpenMStoMSstatsFormatOpenMStoMSstatsTMTFormatOpenSWATHtoMSstatsFormatPDtoMSstatsFormatPDtoMSstatsTMTFormatPhilosophertoMSstatsTMTFormatProgenesistoMSstatsFormatProteinProspectortoMSstatsTMTFormatSkylinetoMSstatsFormatSpectroMinetoMSstatsTMTFormatSpectronauttoMSstatsFormat

Dependencies:backportscheckmatedata.tablelog4rRcppstringi

Working with MSstatsConvert

Rendered frommsstats_data_format.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2020-10-01
Started: 2020-10-01

Readme and manuals

Help Manual

Help pageTopics
Clean raw Proteome Discoverer data.cleanRawPD
Convert output of converters to data.frameas.data.frame.MSstatsValidated
Convert output of converters to data.tableas.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 filesDIANNtoMSstatsFormat
Import DIA-Umpire filesDIAUmpiretoMSstatsFormat
Import FragPipe filesFragPipetoMSstatsFormat
Get one of files contained in an instance of 'MSstatsInputFiles' class.getInputFile getInputFile,MSstatsInputFiles-method getInputFile,MSstatsPhilosopherFiles-method
Import MaxQuant filesMaxQtoMSstatsFormat
Generate MSstatsTMT required input format from MaxQuant outputMaxQtoMSstatsTMTFormat
Import Metamorpheus filesMetamorpheusToMSstatsFormat
Run Anomaly ModelMSstatsAnomalyScores
Creates balanced design by removing overlapping fractions and filling incomplete rowsMSstatsBalancedDesign
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 processingMSstatsLogsSettings
Create annotationMSstatsMakeAnnotation
Preprocess outputs from MS signal processing tools for analysis with MSstatsMSstatsPreprocess
Save session informationMSstatsSaveSessionInfo
Import OpenMS filesOpenMStoMSstatsFormat
Generate MSstatsTMT required input format for OpenMS outputOpenMStoMSstatsTMTFormat
Import OpenSWATH filesOpenSWATHtoMSstatsFormat
Import Proteome Discoverer filesPDtoMSstatsFormat
Convert Proteome Discoverer output to MSstatsTMT format.PDtoMSstatsTMTFormat
Convert Philosopher (Fragpipe) output to MSstatsTMT format.PhilosophertoMSstatsTMTFormat
Import Progenesis filesProgenesistoMSstatsFormat
Generate MSstatsTMT required input format from Protein Prospector outputProteinProspectortoMSstatsTMTFormat
Import Skyline filesSkylinetoMSstatsFormat
Import data from SpectroMineSpectroMinetoMSstatsTMTFormat
Import Spectronaut filesSpectronauttoMSstatsFormat