PXD012414 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-01-17 04:27:12 | ID requested | |
⏵ 1 | 2019-03-28 13:46:03 | announced | |
Publication List
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] |
Keyword List
curator keyword: Biomedical |
submitter keyword: Urinary tract infection, Innate immune response, Inflammation, Neutrophil infiltration, Urine diagnostics, Proteomics, Metaproteomics, Gardnerella, Klebsiella, Uropathogen |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD012414
- Label: PRIDE project
- Name: Diagnosing inflammation and infection in the urinary system via proteomics