Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31316139", "kind": "science-record", "revision": 5, "content_hash": "sha256:3ca8d9283c6112ecbf5169161c2f0ab08d0a77b7cd6fc35df02bfa7881c1d5b9", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T18:51:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells.", "doi": "10.1038/s41598-019-46897-z", "pmid": "31316139", "authors": ["Iulia M Lazar", "Arba Karcini", "Shreya Ahuja", "Carly Estrada-Palma"], "journal": "Scientific reports", "year": 2019, "abstract": "Cancer evolves as a result of an accumulation of mutations and chromosomal aberrations. Developments in sequencing technologies have enabled the discovery and cataloguing of millions of such mutations. The identification of protein-level alterations, typically by using reversed-phase protein arrays or mass spectrometry, has lagged, however, behind gene and transcript-level observations. In this study, we report the use of mass spectrometry for detecting the presence of mutations-missense, indels and frame shifts-in MCF7 and SKBR3 breast cancer, and non-tumorigenic MCF10A cells. The mutations were identified by expanding the database search process of raw mass spectrometry files by including an in-house built database of mutated peptides (XMAn-v1) that complemented a minimally redundant, canonical database of Homo sapiens proteins. The work resulted in the identification of nearly 300 mutated peptide sequences, of which ~50 were characterized by quality tandem mass spectra. We describe the criteria that were used to select the mutated peptide sequences, evaluate the parameters that characterized these peptides, and assess the artifacts that could have led to false peptide identifications. Further, we discuss the functional domains and biological processes that may be impacted by the observed peptide alterations, and how protein-level detection can support the efforts of identifying cancer driving mutations and genes. Mass spectrometry data are available via ProteomeXchange with identifier PXD014458.", "claims": [{"id": "claim-data-access", "statement": "Data analyzed in this study are included in the Supplementary Information files that include: full list of peptides with altered amino acid sequences, peptide characteristics and Proteome Discoverer search parameters; spectral count data for the mutated peptides, non-mutated counterparts and parent proteins; matches to cancer driver genes and protein variants; full tandem mass spectra of selected peptides. 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In this study, we report the use of mass spectrometry for detecting the presence of mutations-miss", "expanding the database search process of raw mass spectrometry files by including an in-house built databas", "ntifying cancer driving mutations and genes. Mass spectrometry data are available via ProteomeXchange with"], "order_basis": "paper_text_order:337", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tations-missense, indels and frame shifts-in MCF7 and SKBR3 breast cancer, and non-tumorigenic", "Methods Materials The breast cancer (MCF7, SKBR3) and nontumorigenic (MCF10) cell line", "rious factors: SKBR3 in McCoy 5 A + FBS 10%; MCF7 in EMEM + bovine insulin 10 μg/mL + FBS 10%;"], "order_basis": "paper_text_order:555", "id": "assay:2"}]}