Evaluating Chromatographic Approaches for the Quantitative Analysis of a Human Proteome on Orbitrap-Based Mass Spectrometry Systems.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30884231", "kind": "science-record", "revision": 4, "content_hash": "sha256:dd4d1c3760b793b7d1d1c75077d22d02e24a027f699437b844a3db9ae2217aa0", "created_at": "2026-11-01T17:32:42Z", "updated_at": "2026-11-01T22:00:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Evaluating Chromatographic Approaches for the Quantitative Analysis of a Human Proteome on Orbitrap-Based Mass Spectrometry Systems.", "doi": "10.1021/acs.jproteome.9b00036", "pmid": "30884231", "authors": ["Ying Zhang", "Zhihui Wen", "Michael P Washburn", "Laurence Florens"], "journal": "Journal of proteome research", "year": 2019, "abstract": "The Orbitrap is now a core component of several different instruments. However, evaluating the capabilities of each system is lacking in the field. Here, we compared the performance of multidimensional protein identification (MudPIT) on Velos Pro Orbitrap and Velos Orbitrap Elite mass spectrometers to reversed phase liquid chromatography (RPLC) on a Q-Exactive Plus and an Orbitrap Fusion Lumos. Using HeLa cell protein digests, we carried out triplicate analyses of 16 different chromatography conditions on four different instrumentation platforms. We first optimized RPLC conditions by varying column lengths, inner diameters, and particle sizes. We found that smaller particle sizes improve results but only with smaller inner diameter microcapillary columns. We then selected one chromatography condition on each system and varied gradient lengths. We used distributed normalized spectral abundance factor (dNSAF) values to determine quantitative reproducibility. With Pearson product-moment correlation coefficient r values routinely above 0.96, single RPLC on both the QE+ and Orbitrap Lumos outperformed MudPIT on the Orbitrap Elite mass spectrometer. In addition, when comparing dNSAF values measured for the same proteins across the different platforms, RPLC on the Orbitrap Lumos had greater sensitivity than MudPIT, as demonstrated by the detection and quantification of histone deacetylase complex components. Data are available via ProteomeXchange with identifier 10.6019/PXD009875.", "claims": [{"id": "claim-method", "statement": "Calculating Pearson correlation coefficients on the averaged dNSAF values for these stringently selected groups of proteins increased the r values to above 0.86 and 0.8 for the pair-wise comparison with the QE+ and OFL datasets, respectively (Table S2F).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30884231", "locator": "sections[16] \"Effect of LC/MS Pipeline on Label-Free dNSAF Quantitation\" paragraph 2", "quote": "Calculating Pearson correlation coefficients on the averaged dNSAF values for these stringently selected groups of proteins increased the r values to above 0.86 and 0.8 for the pair-wise comparison with the QE+ and OFL datasets, respectively (Table S2F)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository32, 33 with the identifiers 10.6019/PXD009875. All original data files underlying this manuscript may also be accessed after publication from the Stowers Original Data Repository at http://www.stowers.org/research/publications/libpb-1303.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30884231", "locator": "sections[10] \"Data Accessibility.\" paragraph 2", "quote": "The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository32, 33 with the identifiers 10.6019/PXD009875. All original data files underlying this manuscript may also be accessed after publication from the Stowers Original Data Repository at http://www.stowers.org/research/publications/libpb-1303."}], "state": "complete"}, {"id": "claim-target-result", "statement": "With Pearson Product-Moment Correlation Coefficients r values routinely above 0.96, single RPLC on both the QE+ and Orbitrap Lumos outperformed MudPIT on the Orbitrap Elite mass spectrometer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:30884231", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "With Pearson Product-Moment Correlation Coefficients r values routinely above 0.96, single RPLC on both the QE+ and Orbitrap Lumos outperformed MudPIT on the Orbitrap Elite mass spectrometer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "With Pearson Product-Moment Correlation Coefficients r values routinely above 0.96, single RPLC on both the QE+ and Orbitrap Lumos outperformed MudPIT on the Orbitrap Elite mass spectrometer.", "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:30884231"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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Using HeLa cell protein digests, we carried out triplic", "EXPERIMENTAL PROCEDURES Materials. HeLa protein digest standard was purchased from P", "s, the first replicates analyses of the 3 μg HeLa analyzed on the OFL with 120, 240, and 360 m", "ok): Table S1: LC-MS/MS analyses of 200ng of HeLa whole cell digests on three different mass s"], "order_basis": "paper_text_order:492", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Mann-Whitney"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}