A proteomic glimpse into human ureter proteome.

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Yet, it is used in clinical diagnostics of several disorders by detecting changes in its components including urinary protein/polypeptide profile. Despite the fact that majority of proteins detected in urine are primarily originated from the urogenital (UG) tract, determining its precise source within the UG tract remains elusive. In this article, we performed a comprehensive analysis of ureter proteome to assemble the first unbiased ureter dataset. Next, we compared these data to urine, urinary exosome, and kidney mass spectrometric datasets. Our result concluded that among 2217 nonredundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, the ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery. All MS data have been deposited in the ProteomeXchange with identifier PXD002620 (http://proteomecentral.proteomexchange.org/dataset/PXD002620).", "claims": [{"id": "claim-method", "statement": "Peptide candidates were filtered to 0.1% FDR and proteins candidates to 1% FDR using DTASelect 21 with a 10‐ppm window.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26442468", "locator": "sections[5] \"p\" paragraph 1", "quote": "Peptide candidates were filtered to 0.1% FDR and proteins candidates to 1% FDR using DTASelect 21 with a 10‐ppm window."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD002620 and 10.6019/PXD002620. 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In addition, all raw data (Thermo.RAW) are also available in the Peptide Atlas repository at ftp://PASS00641:ZI6249ae@ftp.peptideatlas.org/ 20."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper’s headline result was that, among 2217 nonredundant ureter proteins, 751 candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein; protein abundance was evaluated with the Exponentially Modified Protein Abundance Index (emPAI), and the mass-spectrometry source data were deposited in ProteomeXchange through the PRIDE partner repository as PXD002620.", "kind": "quantitative", "target": {"value": 33.8, "unit": "per cent", "tolerance": null, "source": "Our result concluded that among 2217 nonredundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein."}, "evidence": [{"asset": "source:pmid:26442468", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our result concluded that among 2217 nonredundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein."}, {"asset": "source:pmid:26442468", "locator": "sections[6] \"p\" paragraph 1", "quote": "As illustrated in Fig. 3, the Exponentially Modified Protein Abundance Index 30, 31 (emPAI) values reflected the overwhelming abundance of these proteins in the urine."}, {"asset": "source:pmid:26442468", "locator": "sections[4] \"p\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD002620 and 10.6019/PXD002620."}, {"asset": "source:pmid:26442468", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All MS data have been deposited in the ProteomeXchange with identifier PXD002620 (http://proteomecentral.proteomexchange.org/dataset/PXD002620)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper’s headline result was that, among 2217 nonredundant ureter proteins, 751 candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein; protein abundance was evaluated with the Exponentially Modified Protein Abundance Index (emPAI), and the mass-spectrometry source data were deposited in ProteomeXchange through the PRIDE partner repository as PXD002620.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26442468"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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