The R for Mass Spectrometry initiative: from raw data to identifications and quantitative proteomics data analysis
Author(s): Laurent Gatto,Sebastian Gibb,Johannes Rainer
Affiliation(s): de Duve Institute, UCLouvain, Belgium
Social media: https://fosstodon.org/@lgatto
The aim of the RforMassSpectrometry initiative (https://www.rformassspectrometry.org/) is to provide efficient, thoroughly documented, tested and flexible R software for the analysis and interpretation of high throughput mass spectrometry assays. In this software demo, we will demonstrate three software packages that are central for proteomics data analysis. - The Spectra package , that defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualise and compare spectra data. - The PSMatch package  allows to load, process and analyse peptide-spectrum matches, and can, among others, explore and deconvolute the peptide-protein (group) relations using adjacency matrices and connected components. - The QFeatures package  provides infrastructure to management and process quantitative features for high-throughput mass spectrometry assay, in particular so across assay levels (such as precursors, peptide spectrum matches, peptides and proteins or protein groups) in a coherent and tractable format. We will conclude by illustrating how the MsExperiment package  can be used to bundle these three types of data together.  Gatto L et al. (2023). _Spectra Infrastructure for Mass Spectrometry Data_, R package version 1.9.15. <https://rformassspectrometry.github.io/Spectra/>.  Gatto L, Rainer J, Gibb S (2023). _PSMatch: Handling and Managing Peptide Spectrum Matches_. R package version 1.3.3, <https://github.com/RforMassSpectrometry/PSM>.  Gatto L, Vanderaa C (2023). _QFeatures: Quantitative features for mass spectrometry data_. R package version 1.9.3, <https://github.com/RforMassSpectrometry/QFeatures>.  Gatto L, Rainer J, Gibb S (2022). _MsExperiment: Infrastructure for Mass Spectrometry Experiments_. R package version 1.0.0, <https://github.com/RforMassSpectrometry/MsExperiment>.