Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39273511", "kind": "science-record", "revision": 1, "content_hash": "sha256:fdcd4fa4df51c1a383f5cd5fb212149579ac9c0c0940b75b135cc2073498e30e", "created_at": "2026-11-01T20:29:26Z", "updated_at": "2026-11-01T20:29:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation.", "doi": "10.3390/ijms25179564", "pmid": "39273511", "authors": ["Pablo Juanes-Velasco", "Carlota Arias-Hidalgo", "Marina L García-Vaquero", "Janet Sotolongo-Ravelo", "Teresa Paíno", "Quentin Lécrevisse", "Alicia Landeira-Viñuela", "Rafael Góngora", "Ángela-Patricia Hernández", "Manuel Fuentes"], "journal": "International journal of molecular sciences", "year": 2024, "abstract": "Immunopeptidomics is the area of knowledge focused on the study of peptides assembled in the major histocompatibility complex (MHC), or human leukocyte antigen (HLA) in humans, which could activate the immune response via specific and selective T cell recognition. Advances in high-sensitivity mass spectrometry have enabled the detailed identification and quantification of the immunopeptidome, significantly impacting fields like oncology, infections, and autoimmune diseases. Current immunopeptidomics approaches primarily focus on workflows to identify immunopeptides from HLA molecules, requiring the isolation of the HLA from relevant cells or tissues. Common critical steps in these workflows, such as cell lysis, HLA immunoenrichment, and peptide isolation, significantly influence outcomes. A systematic evaluation of these steps led to the creation of an 'Immunopeptidome Score' to enhance the reproducibility and robustness of these workflows. This score, derived from LC-MS/MS datasets (ProteomeXchange identifier PXD038165), in combination with available information from public databases, aids in optimizing the immunopeptidome characterization process. The 'Immunopeptidome Score' has been applied in a systematic analysis of protein extraction, HLA immunoprecipitation, and peptide recovery yields across several tumor cell lines enabling the selection of peptides with optimal features and, therefore, the identification of potential biomarker and therapeutic targets.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [108] partner repository with the dataset identifier PXD038165 and 10.6019/PXD038165.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39273511", "locator": "sections[37] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [108] partner repository with the dataset identifier PXD038165 and 10.6019/PXD038165."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Immunoaffinity Matrix #2 identified substantially more peptides than Immunoaffinity Matrix #1: 6607–9389 peptides versus 526–5592 peptides, respectively.", "kind": "quantitative", "target": {"value": 10.0, "unit": "per cent", "tolerance": null, "source": "Between 526 and 5592 peptides (5–10% de novo peptides) were observed with Immunoaffinity Matrix #1 while between 6607 and 9389 peptides (7–10% de novo peptides) were observed with Immunoaffinity Matrix #2 (Figure 1 and Table 1)."}, "evidence": [{"asset": "source:pmid:39273511", "locator": "sections[3] \"2.1. Identification of Immunogenic Peptides Assembled in HLA-I\" paragraph 5", "quote": "Between 526 and 5592 peptides (5–10% de novo peptides) were observed with Immunoaffinity Matrix #1 while between 6607 and 9389 peptides (7–10% de novo peptides) were observed with Immunoaffinity Matrix #2 (Figure 1 and Table 1)."}, {"asset": "source:pmid:39273511", "locator": "sections[3] \"2.1. Identification of Immunogenic Peptides Assembled in HLA-I\" paragraph 2", "quote": "Overall, a higher number of proteins and peptides (encoding for those proteins) was identified in the studied samples by Immunoaffinity Matrix #2 and compared to those identified by Immunoaffinity Matrix #1 (Figure 1, Table 1 and Supplementary Table S1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Immunoaffinity Matrix #2 identified substantially more peptides than Immunoaffinity Matrix #1: 6607–9389 peptides versus 526–5592 peptides, respectively.", "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:39273511"], "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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