Mass spectrometry-based proteomics/metabolomics and Bioconductor: from the early days to 2024

Author(s): Laurent Gatto,Sebastian Gibb,Johannes Rainer

Affiliation(s): de Duve Institute, UCLouvain, Belgium



The Bioconductor project has always been best known for its state-of-the-art infrastructure for genomics data analysis and comprehension. Starting with packages for microarrays, and later RNA Sequencing, transcriptomics has been the most visible part of the Bioconductor iceberg. Proteomics has been part of the early days of the project, with the *PROcess* package to process SELDI-TO-MS data, that was cited/documented in the very first Bioconductor paper (2004) and monograph (2005). Proteomics and metabolomics have grown substantially since these early days, both in terms of packages, community contributions, and user base, culminating in the *R for Mass Spectrometry* initiative. In this short talk, I will provide an overview of how the mass spectrometry-based proteomics and metabolomics infrastructure has evolved since the early days, and what the goals for the future are.