Development of an Optimized LC-MS Workflow for Host Cell Protein Characterization to Support Upstream Process Development.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39701585", "kind": "science-record", "revision": 2, "content_hash": "sha256:8c620b8ea0e0fd7f53dea951f46b756db72a9ca76a785c3b8d067cf72915cbe6", "created_at": "2026-11-01T20:30:01Z", "updated_at": "2026-11-01T21:34:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of an Optimized LC-MS Workflow for Host Cell Protein Characterization to Support Upstream Process Development.", "doi": "10.1021/acs.jproteome.4c00637", "pmid": "39701585", "authors": ["Janik D Seidel", "Mark R Condina", "Manuela Klingler-Hoffmann", "Clifford Young", "Leigh Donnellan", "Craig Kyngdon", "Peter Hoffmann"], "journal": "Journal of proteome research", "year": 2025, "abstract": "Host cell proteins (HCPs) coexpressed during the production of biotherapeutics can affect the safety, efficacy, and stability of the final product. As such, monitoring HCP populations and amounts throughout the production and purification process is an essential part of the overall quality control framework. Mass spectrometry (MS) is used as an orthogonal method to enzyme-linked immunosorbent assays (ELISA) for the simultaneous identification and quantification of HCPs, particularly for the analysis of downstream processes. In this study, we present an MS-based analytical protocol with improvements in both speed and identification performance that can be implemented for routine analysis to support upstream process development. The protocol adopts a streamlined sample preparation strategy, combined with a high-throughput MS analysis pipeline. The developed method identifies and quantifies over 1000 HCPs, including 20 proteins listed as high risk in the literature, in a clarified cell culture sample with repeatability and precision shown for digest replicates. In addition, we explore the effects of varying standard spike-ins and changes to the data processing pipeline on absolute quantification estimates of the HCPs, which highlight the importance of standardization for wider use in the industry. Data are available via ProteomeXchange with the identifier PXD053035.", "claims": [{"id": "claim-method", "statement": "The results show almost identical density distributions of quantified HCPs (Figure 2a), and Pearson correlation analysis indicated high reproducibility (Pearson r ≥ 0.98 for all comparisons) (Figure 2b).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39701585", "locator": "sections[18] \"Method Repeatability and Performance\" paragraph 2", "quote": "The results show almost identical density distributions of quantified HCPs (Figure 2a), and Pearson correlation analysis indicated high reproducibility (Pearson r ≥ 0.98 for all comparisons) (Figure 2b)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with the identifier PXD053035.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39701585", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with the identifier PXD053035."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The developed method identifies and quantifies over 1000 HCPs, including 20 proteins listed as high risk in the literature, in a clarified cell culture sample with repeatability and precision shown for digest replicates.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39701585", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The developed method identifies and quantifies over 1000 HCPs, including 20 proteins listed as high risk in the literature, in a clarified cell culture sample with repeatability and precision shown for digest replicates."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The developed method identifies and quantifies over 1000 HCPs, including 20 proteins listed as high risk in the literature, in a clarified cell culture sample with repeatability and precision shown for digest replicates.", "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:39701585"], "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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