Dataset Information

Comprehensive Metaproteomic Analyses of Urine

ABSTRACT: We profiled both fractions of the urinary proteome for 33 human subjects with varied pathologies such as urinary tract infection (UTI), urogenital injury and commensal bacteria colonization. Using a LC-MS/MS based metaproteomic approach, we identified 5,327 non-redundant human proteins, 2,638 and 4,379 of which were associated with soluble urine (SU) and urinary pellet (UP) fractions, respectively, and approximately 1,206 non-redundant protein orthology groups derived from pathogens and commensal organisms of the urogenital tract

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

SUBMITTER: Yanbao Yu

LAB HEAD: Yanbao Yu

PROVIDER: PXD002533 | Pride | 2018-05-24

REPOSITORIES: Pride

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Publications

Comprehensive Metaproteomic Analyses of Urine in the Presence and Absence of Neutrophil-Associated Inflammation in the Urinary Tract.

Yu Yanbao Y Sikorski Patricia P Smith Madeline M Bowman-Gholston Cynthia C Cacciabeve Nicolas N Nelson Karen E KE Pieper Rembert R

Theranostics 20170101 2

Inflammation in the urinary tract results in a urinary proteome characterized by a high dynamic range of protein concentrations and high variability in protein content. This proteome encompasses plasma proteins not resorbed by renal tubular uptake, renal secretion products, proteins of immune cells and erythrocytes derived from trans-urothelial migration and vascular leakage, respectively, and exfoliating urothelial and squamous epithelial cells. We examined how such proteins partition into solu ...[more]

PMID: 28042331

Similar Datasets

Project description:Pseudomonas aeruginosa is one of the most frequent pathogen dominant in complicated urinary tract infections (UTI). To unravel the adaptation strategies of P. aeruginosa to the conditions in the urinary tract and to define the underlying regulatory network an artificial growth system mimicking the conditions in the urinary tract was established. Transcriptome analyses were used to investigate the physiological status of P. aeruginosa under this conditions. We performed comparisons to identify genes induced under artificial urinary tract conditions to unravel the adaptive strategies and the underlying regulatory network used by Pseudomonas aeruginosa during urinary tract infections using Affimetrix GeneChips. Pseudomonas aeruginosa wild type strain PAO1 was grown in an artificial in vitro growth system mimicking the conditions in the urinary tract. Therefore, biofilms were grown on the surface of membrane filters placed on agar plates at 37 Â°C up to the late logarithmic state under aerobic and anaerobic conditions (incubated in an anaerobic beanch). An artificial urine medium (AUM) simulating the averaged urine of an human adult was used as nutrient souce. 10-fold diluted Luria Bertani (LB)-medium was used as reference medium. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. The biofilms were harveted at this time points and resuspsended in 0.9% (w/v) NaCl. The OD578 of biofilm suspension was 0.8 for all tested conditions. First comparison: Identification of genes induced or repressed under aerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown aerobically for 18 h to the late logarithmic phase in biofilms on AUM with the transcriptome profile of the PAO1 strain, which was grown aerobically for 18 h to the late logarithmic phase in biofilms on 10-fold diluted LB. Second comparison: Identification of genes induced or repressed under anaerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown anaerobically for 2 days up to the late logarithmic phase in biofilms on AUM supplemented with 50 mM nitrate with the transcriptome profile of the PAO1 strain, which was grown anaerobically for 2 days up to the late logarithmic phase in biofilms on 10-fold diluted LB supplemented with 50 mM nitrate.

			Action	DRS
	UP_10_rep1.msf	Msf
	UP_10_rep1.raw	Raw
	UP_10_rep2.msf	Msf
	UP_10_rep2.raw	Raw
	UP_11_rep1.msf	Msf