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[Short Communication] DiagnoTop: A Computational Pipeline for Discriminating Bacterial Pathogens without Database Search

Abstract : Pathogen identification is crucial to confirm bacterial infections and guide antimicrobial therapy. Although MALDI-TOF mass spectrometry (MS) serves as foundation for tools that enable rapid microbial identification, some bacteria remain challenging to identify. We recently showed that top-down proteomics (TDP) could be used to discriminate closely related enterobacterial pathogens (Escherichia coli, Shigella, and Salmonella) that are indistinguishable with tools rooted in the MALDI-TOF MS approach. Current TDP diagnostic relies on the identification of specific proteoforms for each species through a database search. However, microbial proteomes are often poorly annotated, which complicates the large-scale identification of proteoforms and leads to many unidentified high-quality mass spectra. Here, we describe a new computational pipeline called DiagnoTop that lists discriminative spectral clusters found in TDP data sets that can be used for microbial diagnostics without database search. Applied to our enterobacterial TDP data sets, DiagnoTop could easily shortlist high-quality discriminative spectral clusters, leading to increased diagnostic power. This pipeline opens new perspectives in clinical microbiology and biomarker discovery using TDP.
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https://hal-pasteur.archives-ouvertes.fr/pasteur-03441711
Contributor : Julia Chamot-Rooke Connect in order to contact the contributor
Submitted on : Tuesday, November 23, 2021 - 11:00:59 AM
Last modification on : Wednesday, December 1, 2021 - 4:40:02 PM

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Diogo Borges Lima, Mathieu Dupré, Marlon Dias Mariano Santos, Paulo Costa Carvalho, Julia Chamot-Rooke. [Short Communication] DiagnoTop: A Computational Pipeline for Discriminating Bacterial Pathogens without Database Search. Journal of The American Society for Mass Spectrometry, Springer Verlag (Germany), 2021, 32 (6), pp.1295-1299. ⟨10.1021/jasms.1c00014⟩. ⟨pasteur-03441711⟩

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