Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues.

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Our team adopted chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic analysis to catalog Chr 9-encoded proteins from normal tissues, lung cancer cell lines, and lung cancer tissues. Approximately 74.7% of the Chr 9 genes of the human genome were identified, which included approximately 28% of missing proteins (46 of 162) on Chr 9 compared with the list of missing proteins from the neXtProt Master Table (2013-09). In addition, we performed a comparative proteomics analysis between normal lung and lung cancer tissues. On the basis of the data analysis, 15 proteins from Chr 9 were detected only in lung cancer tissues. Finally, we conducted a proteogenomic analysis to discover Chr 9-residing single nucleotide polymorphisms (SNP) and mutations described in the COSMIC cancer mutation database. We identified 21 SNPs and four mutations containing peptides on Chr 9 from normal human cells/tissues and lung cancer cell lines, respectively. In summary, this study provides valuable information of the human proteome for the scientific community as part of C-HPP. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000603.", "claims": [{"id": "claim-target-result", "statement": "Using a 1% false discovery rate, the proteogenomic analysis identified 21 SNP-containing peptides and four mutation-containing peptides from Chr 9 proteins.", "kind": "quantitative", "target": {"value": 1.0, "unit": "per cent", "tolerance": null, "source": "At a 1% FDR, peptides with SNPs or mutations derived from Chr 9 were collected for further analysis."}, "evidence": [{"asset": "source:pmid:24274035", "locator": "sections[7] \"Identification of SNPs and mutation on Chr 9\" paragraph 2", "quote": "At a 1% FDR, peptides with SNPs or mutations derived from Chr 9 were collected for further analysis."}, {"asset": "source:pmid:24274035", "locator": "sections[12] \"Identification of SNP- and mutation-containing peptides derived from Chr 9-encoded proteins\" paragraph 2", "quote": "We identified 249 SNPs on Chr 9 genes from normal human cells/tissues, with 21 SNP-containing peptides being mapped to 19 genes that were identified from normal adult lung tissue."}, {"asset": "source:pmid:24274035", "locator": "sections[12] \"Identification of SNP- and mutation-containing peptides derived from Chr 9-encoded proteins\" paragraph 2", "quote": "In addition, we observed four peptides from the two lung cancer cell lines that contained amino acid substitutions, which could be explained on the basis of mutations in the COSMIC database."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using a 1% false discovery rate, the proteogenomic analysis identified 21 SNP-containing peptides and four mutation-containing peptides from Chr 9 proteins.", "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:24274035"], "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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