Functional annotation of proteome encoded by human chromosome 22.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24669763", "kind": "science-record", "revision": 6, "content_hash": "sha256:d39a254816ea1c5a256ccc940df790d8609875a6f09a9e16c9caf7211e1236e9", "created_at": "2026-11-01T15:40:04Z", "updated_at": "2026-11-01T21:19:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Functional annotation of proteome encoded by human chromosome 22.", "doi": "10.1021/pr401169d", "pmid": "24669763", "authors": ["Sneha M Pinto", "Srikanth S Manda", "Min-Sik Kim", "KyOnese Taylor", "Lakshmi Dhevi Nagarajha Selvan", "Lavanya Balakrishnan", "Tejaswini Subbannayya", "Fangfei Yan", "T S Keshava Prasad", "Harsha Gowda", "Charles Lee", "William S Hancock", "Akhilesh Pandey"], "journal": "Journal of proteome research", "year": 2014, "abstract": "As part of the chromosome-centric human proteome project (C-HPP) initiative, we report our progress on the annotation of chromosome 22. Chromosome 22, spanning 51 million base pairs, was the first chromosome to be sequenced. Gene dosage alterations on this chromosome have been shown to be associated with a number of congenital anomalies. In addition, several rare but aggressive tumors have been associated with this chromosome. A number of important gene families including immunoglobulin lambda locus, Crystallin beta family, and APOBEC gene family are located on this chromosome. On the basis of proteomic profiling of 30 histologically normal tissues and cells using high-resolution mass spectrometry, we show protein evidence of 367 genes on chromosome 22. Importantly, this includes 47 proteins, which are currently annotated as \"missing\" proteins. We also confirmed the translation start sites of 120 chromosome 22-encoded proteins. Employing a comprehensive proteogenomics analysis pipeline, we provide evidence of novel coding regions on this chromosome which include upstream ORFs and novel exons in addition to correcting existing gene structures. We describe tissue-wise expression of the proteins and the distribution of gene families on this chromosome. These data have been deposited to ProteomeXchange with the identifier PXD000561.", "claims": [{"id": "claim-method", "statement": "The data were also searched against a decoy database, and the results were used to estimate q values using the Percolator algorithm16 within Proteome Discoverer. 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Peptides were considered identified at a q value <0.01 and used for further analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository54 with the data set identifier PXD000561.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24669763", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository54 with the data set identifier PXD000561."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Proteomic profiling of 30 histologically normal tissues and cells by high-resolution mass spectrometry provided protein evidence for 367 chromosome 22 genes, including 47 previously “missing” proteins and confirmation of 120 translation start sites; the source data were deposited in ProteomeXchange under identifier PXD000561.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:24669763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "On the basis of proteomic profiling of 30 histologically normal tissues and cells using high-resolution mass spectrometry, we show protein evidence of 367 genes on chromosome 22."}, {"asset": "source:pmid:24669763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Importantly, this includes 47 proteins, which are currently annotated as “missing” proteins."}, {"asset": "source:pmid:24669763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We also confirmed the translation start sites of 120 chromosome 22-encoded proteins."}, {"asset": "source:pmid:24669763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These data have been deposited to ProteomeXchange with the identifier PXD000561."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Proteomic profiling of 30 histologically normal tissues and cells by high-resolution mass spectrometry provided protein evidence for 367 chromosome 22 genes, including 47 previously “missing” proteins and confirmation of 120 translation start sites; the source data were deposited in ProteomeXchange under identifier PXD000561.", "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:24669763"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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