PXD053994

PXD053994 is an original dataset announced via ProteomeXchange.

Title	A Simplified Method for Comprehensive Capture of the Staphylococcus aureus Proteome
Description	Staphylococcus aureus is major human pathogen causing severe and invasive infections in both community and healthcare settings. Although well studied, a comprehensive exploration of its dynamic and adaptive proteome is still somewhat lacking. Herein we employ streamlined liquid- and gas-phase fractionation with PASEF analysis on a TIMS-TOF instrument to expand coverage and explore the dark proteome of S. aureus. In so doing, we captured the most comprehensive S. aureus proteome to date, totaling 2,231 proteins (85.6% proteome coverage), and did so using a significantly simplified process, requiring less samples and input material. Furthermore, we demonstrated the utility of this library within the context of differential expression profiling by investigating the temporal dynamics of the S. aureus proteome. Notably, a significant portion of the library (94%) and related proteome (80.5%) was characterized by DIA-based proteomic analysis, where we noted alterations in metabolic/biosynthetic processes, ATP production, RNA processing, and an increase in stress response proteins such as chaperones and repair enzymes as cultures progressed into stationary phase. Collectively, our study shines new light on the hidden S. aureus proteome, generating a valuable new resource to the scientific community to facilitate further study of this dangerous human pathogen.
HostingRepository	PRIDE
AnnounceDate	2025-03-31
AnnouncementXML	Submission_2025-03-31_13:42:19.463.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stanley Stevens
SpeciesList	scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-16 23:50:40	ID requested
⏵ 1	2025-03-31 13:42:19	announced

10.1101/2024.08.07.607079;

submitter keyword: gas-phase fractionation, proteomics, DIA-PASEF, DDA-PASEF,Staphylococcus aureus, ion mobility

Stanley Stevens
contact affiliation	University of South Florida
contact email	smstevens@usf.edu
lab head
Stanley Stevens
contact affiliation	University of South Florida
contact email	smstevens@usf.edu
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/2025/03/PXD053994

PRIDE project URI

• PRIDE
  1. PXD053994
     1. Label: PRIDE project
     2. Name: A Simplified Method for Comprehensive Capture of the Staphylococcus aureus Proteome