PXD038928

PXD038928 is an original dataset announced via ProteomeXchange.

Title	Mass Spectrometry-Based Proteomic Profiling of Sonicate Fluid Differentiates Staphylococcus aureus Periprosthetic Joint Infection from Non-Infectious Failure: A pilot study
Description	This study aims to use proteomic profiling of sonicate fluid samples to compare host response during Staphylococcus aureus-associated periprosthetic joint infection (PJI) and non-infected arthroplasty failure (NIAF) and investigate novel biomarkers to increase diagnostic accuracy. In this pilot study, eight sonicate fluid samples (four from NIAF and four from caused by Staphylococcus aureus PJI) were studied. Samples were reduced, alkylated and trypsinized overnight, followed by analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a high-resolution Orbitrap Eclipse mass spectrometer. MaxQuant software suite was used for protein identification, filtering, and label free quantitation. Principal component analysis of the identified proteins clearly separated S. aureus PJI and NIAF samples. Overall, 810 proteins were quantified in any three samples from each group and 35 statistically significant differentially abundant proteins (DAPs) were found (2-sample t-test p-values ≤0.05 and log2fold-change values ≥2 or ≤-2). Gene ontology pathway analysis found that microbial defense responses, specifically those related to neutrophil activation, were increased in S. aureus PJI compared to NIAF samples. Proteomic profiling of sonicate fluid using LC-MS/MS, alone or in combination with complementary protein analyses, differentiated S. aureus PJI and NIAF in this pilot study.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:07:42.854.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-19 03:46:46	ID requested
1	2023-10-24 11:33:11	announced
⏵ 2	2023-11-14 09:08:01	announced	2023-11-14: Updated project metadata.

Fisher CR, Mangalaparthi KK, Greenwood-Quaintance KE, Abdel MP, Pandey A, Patel R, Mass spectrometry-based proteomic profiling of sonicate fluid differentiates Staphylococcus aureus periprosthetic joint infection from non-infectious failure: A pilot study. Proteomics Clin Appl, 17(5):e2200071(2023) [pubmed]

submitter keyword: periprosthetic joint infection, total joint arthroplasty,Label-free quantitation, quantitative proteomics, sonicate fluid

Akhilesh Pandey
contact affiliation	Professor Department of Laboratory Medicine and Pathology Mayo Clinic, Rochester Minnesota - 55901, USA
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.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/2023/10/PXD038928

PRIDE project URI

• PRIDE
  1. PXD038928
     1. Label: PRIDE project
     2. Name: Mass Spectrometry-Based Proteomic Profiling of Sonicate Fluid Differentiates Staphylococcus aureus Periprosthetic Joint Infection from Non-Infectious Failure: A pilot study