Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification
Mass spectrometry-based proteomics has revolutionized bacterial identification and elucidated many molecular mechanisms underlying bacterial growth, community formation, and drug resistance. However, most research has been focused on a few model bacteria, overlooking bacterial diversity. In this study, we present the most extensive bacterial proteomic resource to date, covering 303 species, 119 genera, and five phyla with over 636,000 unique expressed proteins, confirming the existence of over 38,700 hypothetical proteins. Accessible via the public resource ProteomicsDB, this dataset enables quantitative exploration of proteins within and across species. Additionally, we developed MS2Bac, a bacterial identification algorithm that queries NCBI's bacterial proteome space in two iterations. MS2Bac achieved over 99% species-level and 89% strain-level accuracy, surpassing methods like MALDI-TOF and FTIR, as demonstrated with food-derived bacterial isolates. MS2Bac also effectively identified bacteria in clinical samples, highlighting the potential of MS-based proteomics as a routine diagnostic tool.
Authors
- Nina Wantia
- Armin Soleymaniniya (ORCID: https://orcid.org/0000-0002-7799-6091)
- Chen Meng (ORCID: https://orcid.org/0000-0002-5968-6719)
- Miriam Abele (ORCID: https://orcid.org/0000-0003-0084-2999)
- Etienne V. Doll (ORCID: https://orcid.org/0000-0002-4041-6233)
- Mathias Wilhelm (ORCID: https://orcid.org/0000-0002-9224-3258)
- Klaus Neuhaus (ORCID: https://orcid.org/0000-0002-6020-2814)
- Bernhard Küster (ORCID: https://orcid.org/0000-0002-9094-1677)
- Mareike Wenning (ORCID: https://orcid.org/0000-0002-7828-0458)
- Florian Bayer (ORCID: https://orcid.org/0000-0001-6489-2835)
- Siegfried Scherer (ORCID: https://orcid.org/0000-0002-0394-9890)
- Christina Ludwig (ORCID: https://orcid.org/0000-0002-6131-7322)
- Nina Lomp
Institutions
- Health and Safety Authority (IE)
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich (DE)
- Technical University of Munich (DE)
- Thermo Fisher Scientific (Norway) (NO)
Publication Details
- Journal
- Molecular & Cellular Proteomics
- Published
- 2025-01-27
- DOI
- https://doi.org/10.1016/j.mcpro.2025.100917
- Citations
- 13
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 10.48
Funders
- European Commission
- Deutsche Forschungsgemeinschaft
- HORIZON EUROPE Framework Programme
- Elitenetzwerk Bayern
- H2020 European Research Council