A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28467808", "kind": "science-record", "revision": 5, "content_hash": "sha256:2fff083b89dbab40e9736384e63c57aea571a4536ce7d13a6415b34d547ee251", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T18:48:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells.", "doi": "10.18632/oncotarget.17076", "pmid": "28467808", "authors": ["Paula Díez", "Nieves Ibarrola", "Rosa M Dégano", "Quentin Lécrevisse", "Arancha Rodriguez-Caballero", "Ignacio Criado", "Wendy G Nieto", "Rafael Góngora", "Marcos González", "Julia Almeida", "Alberto Orfao", "Manuel Fuentes"], "journal": "Oncotarget", "year": 2017, "abstract": "A wide variety of immunoglobulins (Ig) is produced by the immune system thanks to different mechanisms (V(D)J recombination, somatic hypermutation, and antigen selection). The profiling of Ig sequences (at both DNA and peptide levels) are of great relevance to developing targeted vaccines or treatments for specific diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably increased the knowledge in Ig sequencing and serum Ig peptide profiling in a high-throughput manner. However, the peptide characterization of membrane-bound Ig (e.g., B-cell receptors, BCR) is still a challenge mainly due to the poor recovery of mentioned Ig.Herein, we have evaluated three different sample processing methods for peptide sequencing of BCR belonging to chronic lymphocytic leukemia (CLL) B cells identifying up to 426 different peptide sequences (MS/MS data are available via ProteomeXchange with identifier PXD004466). Moreover, as a consequence of the results here obtained, recommended guidelines have been described for BCR-sequencing of B-CLL samples by MS approaches.For this purpose, an in-house algorithm has been designed and developed to compare the MS/MS results with those obtained by molecular biology in order to integrate both proteomics and genomics results and establish the steps to follow when sequencing membrane-bound Ig by MS/MS.", "claims": [{"id": "claim-data-access", "statement": "The MS data along with the identification results have been deposited to the ProteomeXchange Consortium via the PRIDE [40] partner repository with the dataset identifier PXD004466.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28467808", "locator": "sections[15] \"Database search\" paragraph 3", "quote": "The MS data along with the identification results have been deposited to the ProteomeXchange Consortium via the PRIDE [40] partner repository with the dataset identifier PXD004466."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Three BCR sample-processing strategies were evaluated for MS/MS peptide sequencing of CLL B cells, identifying up to 426 distinct peptide sequences; the underlying MS/MS data are available through ProteomeXchange under PXD004466. No inferential statistical method is stated in the paper.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28467808", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Herein, we have evaluated three different sample processing methods for peptide sequencing of BCR belonging to chronic lymphocytic leukemia (CLL) B cells identifying up to 426 different peptide sequences (MS/MS data are available via ProteomeXchange with identifier PXD004466)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Three BCR sample-processing strategies were evaluated for MS/MS peptide sequencing of CLL B cells, identifying up to 426 distinct peptide sequences; the underlying MS/MS data are available through ProteomeXchange under PXD004466. No inferential statistical method is stated in the paper.", "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:28467808"], "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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Sample collection Peripheral blood (PB) B-l", "c diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequenci", "molecular biology in order to integrate both proteomics and genomics results and establish the steps"], "order_basis": "paper_text_order:424", "id": "assay:1"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notab", "hniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably in"], "order_basis": "paper_text_order:456", "id": "assay:2"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["lamanca [26]. High-sensitive multi-parameter flow cytometry was performed for the immunophenotyping of c"], "order_basis": "paper_text_order:6484", "id": "assay:3"}]}