PXD000156

PXD000156 is an original dataset announced via ProteomeXchange.

Title	Tryptic striptease of Staphylococcus aureus unveils the cell surface localization of immunodominant epitopes
Description	The opportunistic pathogen Staphylococcus aureus has become a major threat for human health and well-being by developing resistance to antibiotics, and by its fast evolution into new lineages that rapidly spread within the healthy human population. This calls for the development of active or passive immunization strategies to prevent or treat acute phase infections. Since no such anti-staphylococcal immunization approaches are available as yet, the present studies were aimed at identifying new leads for their development. For this purpose, we thoroughly profiled the cell surface-exposed staphylococcal proteome by combining two surface shaving approaches. In parallel, non-covalently cell wall-bound proteins were extracted with KSCN and analyzed by gel-free proteomics, and also the exoproteome was analyzed through gel-free proteomics. Lastly, we screened a selection of the identified cell wall-attached proteins for binding of immunoglobulin G from patients that have been challenged with different types of S. aureus over extended periods of time due to chronic wound colonization. The combined results of these analyses highlight particular cell surface-exposed S. aureus proteins with highly immunogenic epitopes as potentially powerful targets for the development of protective anti-staphylococcal immunization strategies. Bioinformatics pipeline: Reduction and alkylation, desalting of the samples, mass spectrometric (MS) analysis and database searches were performed as previously described (PMID: 20662103). The strain-specific uniprot databases were used for the /S. aureus/ strains Newman and USA300, respectively including concatenated reversed databases with 5250 and 5298 entries. Validation of MS/MS-based peptide and protein identifications was performed with Scaffold (version Scaffold_2_04_00, Proteome Software Inc., Portland, OR). Peptide identifications were accepted if they exceeded the specific database search engine thresholds. Sequest identifications required at least deltaCn scores of greater than 0.10 and XCorr scores of greater than 1.9, 2.2, 3.8 and 3.8 for singly, doubly, triply and quadruply charged peptides, respectively. All experiments were conducted in independent triplicates. Peptides were only accepted as identified if they were detected in at least two out of the three replicates per sample set. With these filter parameters no false positive hits were obtained.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:07:31.036.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Otto
SpeciesList	scientific name: Staphylococcus aureus (strain USA300); NCBI TaxID: 367830; scientific name: Staphylococcus aureus (strain Newman); NCBI TaxID: 426430;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-02-21 08:21:23	ID requested
1	2020-06-18 22:29:28	announced
⏵ 2	2024-10-22 05:07:35	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.0c00043;

Dreisbach A, Wang M, van der Kooi-Pol MM, Reilman E, Koedijk DGAM, Mars RAT, Duipmans J, Jonkman M, Benschop JJ, Bonarius HPJ, Groen H, Hecker M, Otto A, B, ä, sell K, Bernhardt J, Back JW, Becher D, Buist G, van Dijl JM, Unveils Immunodominant Epitopes on the Bacterial Cell Surface. J Proteome Res, 19(8):2997-3010(2020) [pubmed]

submitter keyword: cellwall, surfacome, exoproteome,Staphylococcus aureus, virulence factor

Andreas Otto
contact affiliation	Institute for Microbiology
contact email	andreas.otto@uni-greifswald.de
lab head
Andreas Otto
contact affiliation	Institute for Microbiology
contact email	andreas.otto@uni-greifswald.de
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/2020/06/PXD000156

PRIDE project URI

• PRIDE
  1. PXD000156
     1. Label: PRIDE project
     2. Name: Tryptic striptease of Staphylococcus aureus unveils the cell surface localization of immunodominant epitopes