Package: MsExperiment 1.9.1

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]

MsExperiment_1.9.1.tar.gz
MsExperiment_1.9.1.zip(r-4.5)MsExperiment_1.9.1.zip(r-4.4)MsExperiment_1.9.1.zip(r-4.3)
MsExperiment_1.9.1.tgz(r-4.5-any)MsExperiment_1.9.1.tgz(r-4.4-any)MsExperiment_1.9.1.tgz(r-4.3-any)
MsExperiment_1.9.1.tar.gz(r-4.5-noble)MsExperiment_1.9.1.tar.gz(r-4.4-noble)
MsExperiment_1.9.1.tgz(r-4.4-emscripten)MsExperiment_1.9.1.tgz(r-4.3-emscripten)
MsExperiment.pdf |MsExperiment.html✨
MsExperiment/json (API)
NEWS

# Install 'MsExperiment' in R:

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

Bug tracker:https://github.com/rformassspectrometry/msexperiment/issues5 issues

On BioConductor:MsExperiment-1.9.1(bioc 3.21)MsExperiment-1.8.0(bioc 3.20)

infrastructure proteomics massspectrometry metabolomics experimentaldesign dataimport

8.51 score 5 stars 14 packages 126 scripts 2.0k downloads 19 exports 109 dependencies

Last updated 1 months agofrom:bc06ba2278. Checks:1 OK, 8 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 14 2025
R-4.5-win	NOTE	Mar 14 2025
R-4.5-mac	NOTE	Mar 14 2025
R-4.5-linux	NOTE	Mar 14 2025
R-4.4-win	NOTE	Mar 14 2025
R-4.4-mac	NOTE	Mar 14 2025
R-4.4-linux	NOTE	Mar 14 2025
R-4.3-win	NOTE	Mar 14 2025
R-4.3-mac	NOTE	Mar 14 2025

Exports:dbWriteSampleData existMsExperimentFiles experimentFiles experimentFiles<-filterSpectra linkSampleData MsExperiment MsExperimentFiles otherData otherData<-qdata qdata<-readMsExperiment sampleData sampleData<-show spectra spectra<-spectraSampleIndex

Dependencies:abind AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel bslib cachem cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dplyr evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mgcv mime MsCoreUtils MultiAssayExperiment munsell nlme openssl pillar pkgconfig plotly plyr promises ProtGenerics purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S4Arrays S4Vectors sass scales snow SparseArray Spectra stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml

Managing Mass Spectrometry Experiments

Rendered fromMsExperiment.Rmdusingknitr::rmarkdownon Mar 14 2025.

Last update: 2024-04-16
Started: 2021-04-16

Citation

To cite package ‘MsExperiment’ in publications use:

Gatto L, Rainer J, Gibb S (2025). MsExperiment: Infrastructure for Mass Spectrometry Experiments. R package version 1.9.1, https://bioconductor.org/packages/MsExperiment.

Corresponding BibTeX entry:

  @Manual{,
    title = {MsExperiment: Infrastructure for Mass Spectrometry
      Experiments},
    author = {Laurent Gatto and Johannes Rainer and Sebastian Gibb},
    year = {2025},
    note = {R package version 1.9.1},
    url = {https://bioconductor.org/packages/MsExperiment},
  }

Development and contributors

Readme and manuals

Managing mass spectrometry experiments

The MsExperiment package provides the MsExperiment class that can be used to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry experiment. This includes

experimental design
data files
raw data: spectra and chromatograms
proteomics identification results and protein database
quantitative features

The respective data handling functionality is handled by dedicated packages such as Spectra for spectra data, QFeatures for quantitative features, Biostrings for fasta files, ...

See the package homepage for more information.

This package is part of the RforMassSpectrometry initiative: https://www.rformassspectrometry.org/

Installation

The package can be installed with

install.packages("BiocManager")
BiocManager::install("MsExperiment")

Contributions

Contributions are highly welcome and should follow the contribution guidelines. Also, please check the coding style guidelines in the RforMassSpectrometry vignette.

Help Manual

Help page	Topics
Write sample annotations to a MsBackendSql SQL database	dbWriteSampleData
Managing Mass Spectrometry Experiments	experimentFiles 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 files	existMsExperimentFiles MsExperimentFiles MsExperimentFiles-class show,MsExperimentFiles-method
Import MS spectra data of an experiment	readMsExperiment