Proteotyping of organisms

We have revolutionized the application of tandem mass spectrometry for pathogen identification, enabling the detection of bacteria or viruses without any prior knowledge. Our in house developed software, µorg.ID, automatically interpret proteomics results, providing a comprehensive list of the species present in a sample and identifying their antibiotic resistances by detecting specific peptides.

We have successfully transferred this methodology to specific laboratories in France engaged in forensics and diagnostics. Moreover, we have been at the forefront of developing rapid mass spectrometry methods for characterizing SARS-CoV-2 and Monkeypox viruses during the recent pandemics. Notably we demonstrated that a 3-min window acquisition is sufficient for identifying discriminative peptides from SARS-CoV-2, facilitating reliable diagnostics.

Gouveia et al., 2020

Innovation continues to drive our efforts, as we have recently invented a novel method for multiplexing a large number of samples without chemical reagent for their identification. This advancement significantly enhances the throughput of tandem mass spectrometry, allowing for the identification of approximately one microorganism per minute, translating to an impressive 10,000 identifications per week. This rate surpasses the capabilities of MALDI-TOF and offer enhanced confidence, even when encountering microorganisms not previously recorded in the database.

  • Lozano C, Grenga L, Gallais F, Miotello G, Bellanger L, Armengaud J (2022) Mass spectrometry detection of Monkeypox virus: comprehensive coverage for ranking the most responsive peptide markers. Proteomics e2200253. doi: 10.1002/pmic.202200253.

  • Lozano C, Kielbasa M, Gaillard JC, Miotello G, Pible O, Armengaud J (2022) Identification and characterization of marine microorganisms by tandem mass spectrometry proteotyping. Microorganisms 10(4):719. doi: 10.3390/microorganisms10040719.

  • Hayoun K, Pible O, Petit P, Allain F, Jouffret V, Culotta K, Rivasseau C, Armengaud J, Alpha-Bazin B (2020) Proteotyping Environmental Microorganisms by Phylopeptidomics: Case Study Screening Water from a Radioactive Material Storage Pool. Microorganisms 8(10):1525.

  • Gouveia D, Miotello G, Gallais F, Gaillard JC, Debroas S, Bellanger L, Lavigne JP, Sotto A, Grenga L, Pible O, Armengaud J (2020) Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window. J Proteome Res 19:4407-4416. doi: 10.1021/acs.jproteome.0c00535.

  • Hayoun K, Gaillard JC, Pible O, Alpha-Bazin B, Armengaud J (2020) High-throughput proteotyping of bacterial isolates by double barrel chromatography-tandem mass spectrometry based on microplate paramagnetic beads and phylopeptidomics. J. Proteomics 226:103887. doi: 10.1016/j.jprot.2020.103887.

  • Gouveia D, Grenga L, Gaillard JC, Gallais F, Bellanger L, Pible O, Armengaud J (2020) Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data. Proteomics. 20(14):e2000107. doi: 10.1002/pmic.202000107.