PXD025436

PXD025436 is an original dataset announced via ProteomeXchange.

Title	Surface-shaving of Staphylococcus aureus strains using Lipid-based Protein Immobilization (LPI) and quantitative proteomic analysis reveal differences in protein expression levels of the surfaceome
Description	Staphylococcus aureus is a pathogen which can cause a wide range of infections. To find new targets for diagnostics and treatment as well as understanding host-pathogen interactions, many studies have focused on the bacterial surface proteins. In the study presented here, bacterial cell surface-shaving, using Lipid-based Protein Immobilization (LPI), followed by tandem mass tag (TMT) protocols for performing relative quantitative mass spectrometry proteomics, was performed to examine the surface proteome (surfaceome) of selected strains of S. aureus. The study included analyses of surface protein-deficient mutants compared to the wildtype S. aureus strain Newman, as well strain isolates of different clinical associations. Quantitative proteomics were applied in the analysis of the surface proteome of Staphylococcus aureus. In study 1, the differential abundance of proteins in the mutant strains ΔClfA, ΔSrtAΔSrtB and ΔSpa was compared to those in the Newman parental strain. All together 7880 peptides were identified in Study 1 corresponding to 1290 proteins, and the results clearly showed that the mutant strains were deficient in the knocked-out genes. The Clinical strains study (Study 2) included the Newman strain, the reference strains LS-1 and SH1000 and three clinical isolates, two from invasive infections and one from mild skin infection. A total of 4949 peptides were identified in Study 2 corresponding to 919 proteins. For each strain, approximately 20 proteins showed higher or lower abundance (fold changes) when compared to the Newman strain. The results indicate that surface shaving of intact bacteria by LPI in combination with protocols for performing quantitative proteomics makes it possible to distinguish differences in protein abundance of the surfaceome, including virulence factors, between S. aureus strains.
HostingRepository	PRIDE
AnnounceDate	2024-10-17
AnnouncementXML	Submission_2024-10-17_03:14:04.430.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Proteomics Core Facility
SpeciesList	scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-16 03:50:34	ID requested
⏵ 1	2024-10-17 03:14:06	announced

10.3390/microorganisms12081725;

Karlsson A, Alarc, ó, n LA, Pi, ñ, eiro-Iglesias B, Jacobsson G, Skovbjerg S, Moore ERB, Kopparapu PK, Jin T, Karlsson R, Strains and Quantitative Proteomic Analysis Reveal Differences in Protein Abundance of the Surfaceome. Microorganisms, 12(8):(2024) [pubmed]

submitter keyword: proteomics, relative quantification, mass spectrometry, virulence factors,Staphylococcus aureus, surfaceome, tandem mass tags

Roger Karlsson
contact affiliation	Department of Infection Diseases, Institute of Biomedicine,Sahlgrenska Academy of the University of Gothenburg
contact email	roger.karlsson@nanoxisconsulting.com
lab head
Proteomics Core Facility
contact affiliation	SAMBIO Core Facilities, Sahgrenska Academy, University of Gothenburg
contact email	gupcf@outlook.com
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/2024/10/PXD025436

PRIDE project URI

• PRIDE
  1. PXD025436
     1. Label: PRIDE project
     2. Name: Surface-shaving of Staphylococcus aureus strains using Lipid-based Protein Immobilization (LPI) and quantitative proteomic analysis reveal differences in protein expression levels of the surfaceome