PXD019247

PXD019247 is an original dataset announced via ProteomeXchange.

Title	Optimization of a Top-Down Proteomics Platform for Closely-Related Pathogenic Bacteria Discrimination
Description	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.
HostingRepository	PRIDE
AnnounceDate	2023-05-15
AnnouncementXML	Submission_2023-05-15_01:48:01.834.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	MagalieDuchateau
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Newport; NCBI TaxID: 108619; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Salmonella enterica subsp. enterica serovar Muenchen; NCBI TaxID: 596; scientific name: Shigella flexneri; NCBI TaxID: 623; scientific name: Escherichia coli O157:H7; NCBI TaxID: 83334; scientific name: Shigella sonnei; NCBI TaxID: 624; scientific name: Salmonella enterica subsp. enterica serovar Enteritidis; NCBI TaxID: 149539; scientific name: Escherichia coli O26:H11; NCBI TaxID: 244319; scientific name: Salmonella enterica subsp. enterica serovar Typhimurium; NCBI TaxID: 90371;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-17 23:56:59	ID requested
1	2020-09-24 01:36:50	announced
⏵ 2	2023-05-15 01:48:02	announced	2023-05-15: Updated project metadata.

Dupr, é M, Duchateau M, Malosse C, Borges-Lima D, Calvaresi V, Podglajen I, Clermont D, Rey M, Chamot-Rooke J, Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination. J Proteome Res, 20(1):202-211(2021) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: Mass Spectrometry, Optimization,Top-Down Proteomics, Bacteria

JuliaChamot-Rooke
contact affiliation	Institut Pasteur - CNRS USR 2000 Mass Spectrometry for Biology Unit 28, rue du Dr. Roux 75 015 Paris
contact email	julia.chamot-rooke@pasteur.fr
lab head
MagalieDuchateau
contact affiliation	Institut Pasteur
contact email	magalie.duchateau@pasteur.fr
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/09/PXD019247

PRIDE project URI

• PRIDE
  1. PXD019247
     1. Label: PRIDE project
     2. Name: Optimization of a Top-Down Proteomics Platform for Closely-Related Pathogenic Bacteria Discrimination