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
  • raw data: spectra
  • raw data: 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, Features for quantitative features, Biostrings for fasta files, …

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