PXD012414

PXD012414 is an original dataset announced via ProteomeXchange.

Title	Diagnosing inflammation and infection in the urinary system via proteomics
Description	Current methodology for the diagnosis of diseases in the urinary system includes patient symptomology, urine analysis and urine culture. Asymptomatic bacteriuria from urethral colonization or indwelling catheters, sample contamination from perineal or vaginal sources, and non-infectious inflammatory conditions can mimic UTIs, leading to uncertainty on medical treatment decisions. Organisms causing more than 98% of all UTIs and commensal microbes of the urogenital and perineal area were identified from 76 urine sediments with detection sensitivities estimated to be similar to urine culture. Proteomic data permitted a thorough evaluation of inflammatory and antimicrobial immune responses. Hierarchical clustering of the data revealed that high abundances of proteins from activated neutrophils were associated with pathogens in most cases, and correlated well with leukocyte esterase activities and leukocyte counts via microscopy. Proteomic data also allowed assessments of urothelial injury, by quantifying proteins highly expressed in red blood cells and contributing to the acute phase response. Lactobacillus and Gardnerella vaginalis were frequently identified suggesting urethral colonization and/or vaginal contamination of urine.
HostingRepository	PRIDE
AnnounceDate	2019-03-28
AnnouncementXML	Submission_2019-03-28_13:46:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yanbao Yu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-17 04:27:12	ID requested
⏵ 1	2019-03-28 13:46:03	announced

Yu Y, Sikorski P, Bowman-Gholston C, Cacciabeve N, Nelson KE, Pieper R, Diagnosing inflammation and infection in the urinary system via proteomics. J Transl Med, 13():111(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: Urinary tract infection, Innate immune response, Inflammation, Neutrophil infiltration, Urine diagnostics, Proteomics, Metaproteomics, Gardnerella, Klebsiella, Uropathogen

Yanbao Yu
contact affiliation	J. Craig Venter Institute, Rockville, MD 20850
contact email	yayu@jcvi.org
lab head
Yanbao Yu
contact affiliation	J. Craig Venter Institute
contact email	yayu@jcvi.org
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/2019/03/PXD012414

PRIDE project URI

• PRIDE
  1. PXD012414
     1. Label: PRIDE project
     2. Name: Diagnosing inflammation and infection in the urinary system via proteomics