Package: MsExperiment 1.14.0

Laurent Gatto

MsExperiment: Infrastructure for Mass Spectrometry Experiments

Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.

Authors:Laurent Gatto [aut, cre], Johannes Rainer [aut], Sebastian Gibb [aut], Tuomas Borman [ctb]

MsExperiment_1.14.0.tar.gz
MsExperiment_1.14.0.zip(r-4.7)MsExperiment_1.14.0.zip(r-4.6)MsExperiment_1.14.0.zip(r-4.5)
MsExperiment_1.14.0.tgz(r-4.6-any)MsExperiment_1.14.0.tgz(r-4.5-any)
MsExperiment_1.14.0.tar.gz(r-4.7-any)MsExperiment_1.14.0.tar.gz(r-4.6-any)
MsExperiment_1.14.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MsExperiment/json (API)
NEWS

# Install 'MsExperiment' in R:
install.packages('MsExperiment', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rformassspectrometry/msexperiment/issues

On BioConductor:MsExperiment-1.15.0(bioc 3.24)MsExperiment-1.14.0(bioc 3.23)

infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport

8.94 score 5 stars 17 packages 307 scripts 1.8k downloads 19 exports 103 dependencies

Last updated from:f47ab3c30c (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING196
linux-devel-x86_64NOTE371
source / vignettesOK1084
linux-release-x86_64NOTE364
macos-release-arm64NOTE265
macos-oldrel-arm64NOTE185
windows-develNOTE463
windows-releaseNOTE458
windows-oldrelNOTE403
wasm-releaseOK248

Exports:dbWriteSampleDataexistMsExperimentFilesexperimentFilesexperimentFiles<-filterSpectralinkSampleDataMsExperimentMsExperimentFilesotherDataotherData<-qdataqdata<-readMsExperimentsampleDatasampleData<-showspectraspectra<-spectraSampleIndex

Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscpp11crosstalkcurldata.tableDBIDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMultiAssayExperimentopensslotelpillarpkgconfigplotlyplyrpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

Managing Mass Spectrometry Experiments

Rendered fromMsExperiment.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-02-06
Started: 2021-04-16

Readme and manuals

Help Manual

Help pageTopics
Write sample annotations to a MsBackendSql SQL databasedbWriteSampleData
Managing Mass Spectrometry ExperimentsexperimentFiles experimentFiles<- filterSpectra,MsExperiment,function-method length,MsExperiment-method linkSampleData MsExperiment MsExperiment-class otherData otherData<- qdata qdata<- sampleData sampleData<- show,MsExperiment-method spectra,MsExperiment-method spectra<-,MsExperiment-method spectraSampleIndex [,MsExperiment,ANY,ANY,ANY-method
A class to store experiment filesexistMsExperimentFiles MsExperimentFiles MsExperimentFiles-class show,MsExperimentFiles-method
Import MS spectra data of an experimentreadMsExperiment