Dataset Information

Optimization of a Top-Down Proteomics Platform for Closely-Related Pathogenic Bacteria Discrimination

ABSTRACT: The current technique used for microbial identification in hospitals is MALDI-TOF MS. However, it suffers from important limitations, in particular for closely-related species or when the database used for the identification lacks the appropriate reference. In this work, we set up a high throughput LC-MS/MS top-down proteomics platform dedicated to intact bacterial protein analysis. Using Escherichia coli as a model, all steps of the workflow were optimized: protein extraction, on-line liquid chromatographic separation, MS/MS fragmentation and data analysis. Using the optimized parameters, about 220 proteins, corresponding to more than 500 proteoforms, could be identified in a single run. We then demonstrated the suitability of the developed platform for the characterization and discrimination of enterobacterial pathogens rather undistinguishable by MALDI-TOF although leading to very different clinical outcomes. For each pathogen, we identified specific proteoforms that could potentially be used as biomarkers. We also improved the characterization of poorly described bacterial strains. Our results highlight the advantage of targeting proteoforms vs peptides for accurate bacterial characterization, and qualify top-down proteomics as a promising tool in clinical microbiology.

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive

ORGANISM(S): Salmonella Enterica Subsp. Enterica Serovar Typhimurium Salmonella Enterica Subsp. Enterica Serovar Muenchen Salmonella Enterica Subsp. Enterica Serovar Enteritidis Escherichia Coli O26:h11 Salmonella Enterica Subsp. Enterica Serovar Newport Shigella Flexneri Shigella Sonnei Escherichia Coli Escherichia Coli O157:h7

SUBMITTER: Magalie Duchateau

LAB HEAD: Julia Chamot-Rooke

PROVIDER: PXD019247 | Pride | 2020-09-24

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20160406_L_VC_ColF18_Exp10_01.raw	Raw
	20160406_L_VC_ColF18_Exp10_02.raw	Raw
	20160406_L_VC_ColF18_Exp11_01.raw	Raw
	20160406_L_VC_ColF18_Exp11_02.raw	Raw
	20160406_L_VC_ColF18_Exp12_01.raw	Raw

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Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination.

Dupré Mathieu M Duchateau Magalie M Malosse Christian C Borges-Lima Diogo D Calvaresi Valeria V Podglajen Isabelle I Clermont Dominique D Rey Martial M Chamot-Rooke Julia J

Journal of proteome research 20201001 1

The current technique used for microbial identification in hospitals is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, it suffers from important limitations, in particular, for closely related species or when the database used for the identification lacks the appropriate reference. In this work, we set up a liquid chromatography (LC)-MS/MS top-down proteomics platform, which aims at discriminating closely related pathogenic bacteria through ...[more]

PMID: 32929970

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