Pilot Evaluation of the Long-Term Reproducibility of Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics of a Complex Proteome Sample.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38417052", "kind": "science-record", "revision": 3, "content_hash": "sha256:271a42148c85425e402d63cfd0d15d44a018250121c56d23353f221ff82fbcd4", "created_at": "2026-11-01T19:20:22Z", "updated_at": "2026-11-01T21:32:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Pilot Evaluation of the Long-Term Reproducibility of Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics of a Complex Proteome Sample.", "doi": "10.1021/acs.jproteome.3c00872", "pmid": "38417052", "authors": ["Seyed Amirhossein Sadeghi", "Wenrong Chen", "Qianyi Wang", "Qianjie Wang", "Fei Fang", "Xiaowen Liu", "Liangliang Sun"], "journal": "Journal of proteome research", "year": 2024, "abstract": "Mass spectrometry (MS)-based top-down proteomics (TDP) has revolutionized biological research by measuring intact proteoforms in cells, tissues, and biofluids. Capillary zone electrophoresis-tandem MS (CZE-MS/MS) is a valuable technique for TDP, offering a high peak capacity and sensitivity for proteoform separation and detection. However, the long-term reproducibility of CZE-MS/MS in TDP remains unstudied, which is a crucial aspect for large-scale studies. This work investigated the long-term qualitative and quantitative reproducibility of CZE-MS/MS for TDP for the first time, focusing on a yeast cell lysate. Over 1000 proteoforms were identified per run across 62 runs using one linear polyacrylamide (LPA)-coated separation capillary, highlighting the robustness of the CZE-MS/MS technique. However, substantial decreases in proteoform intensity and identification were observed after some initial runs due to proteoform adsorption onto the capillary inner wall. To address this issue, we developed an efficient capillary cleanup procedure using diluted ammonium hydroxide, achieving high qualitative and quantitative reproducibility for the yeast sample across at least 23 runs. The data underscore the capability of CZE-MS/MS for large-scale quantitative TDP of complex samples, signaling its readiness for deployment in broad biological applications. The MS RAW files were deposited in ProteomeXchange Consortium with the data set identifier of PXD046651.", "claims": [{"id": "claim-method", "statement": "The intensities of overlapped proteoforms between any two runs were used to create the Pearson linear correlation and obtain the correlation coefficients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38417052", "locator": "sections[11] \"Reproducibility of CZE-MS/MS for Top-Down Proteomics of a Complex Sample\" paragraph 9", "quote": "The intensities of overlapped proteoforms between any two runs were used to create the Pearson linear correlation and obtain the correlation coefficients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00872.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38417052", "locator": "sections[15] \"Supporting Information Available\" paragraph 2", "quote": "The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00872."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A capillary cleanup procedure enabled high qualitative and quantitative reproducibility of CZE-MS/MS measurements across at least 23 runs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38417052", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To address this issue, we developed an efficient capillary cleanup procedure using diluted ammonium hydroxide, achieving high qualitative and quantitative reproducibility for the yeast sample across at least 23 runs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A capillary cleanup procedure enabled high qualitative and quantitative reproducibility of CZE-MS/MS measurements across at least 23 runs.", "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:38417052"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD046651"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD046651"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38417052", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1021/acs.jproteome.3c00872", "sha256": "sha256:ab2a2251a14f867e5330a91c44931b5cd2979dcfe77358f65d7743a0c0f13939", "bytes": 42574, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1021/acs.jproteome.3c00872", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11002928", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD046651", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD046651", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD046651", "version": null, "note": "The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00872.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00872.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Pilot evaluation of long-term reproducibility of capillary zone electrophoresis-tandem mass spectrometry for top-down proteomics of a complex proteome sample", "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD046651 not downloaded", "asset:data:geo:PXD046651 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-2", "family": null, "specific": null, "label": "Pairwise Pearson linear correlation of proteoform intensities", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The intensities of overlapped proteoforms between any two runs were used to create the Pearson linear correlation and obtain the correlation coefficients."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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