Proteomic profiling of idiopathic Parkinson's disease primary patient cells by SWATH-MS.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35579911", "kind": "science-record", "revision": 2, "content_hash": "sha256:5d16afd5bd3228b9042a24e454143e0d138114170a1c1c15695ba76076e669e8", "created_at": "2026-11-01T18:14:28Z", "updated_at": "2026-11-01T18:58:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic profiling of idiopathic Parkinson's disease primary patient cells by SWATH-MS.", "doi": "10.1002/prca.202200015", "pmid": "35579911", "authors": ["Stephen A Wood", "Peter G Hains", "Arnaud Muller", "Melissa Hill", "Susitha Premarathne", "Mariyam Murtaza", "Phillip J Robinson", "George D Mellick", "Alex M Sykes"], "journal": "Proteomics. Clinical applications", "year": 2022, "abstract": "PURPOSE: Parkinson's disease (PD) is the second most prevalent neurodegenerative disease. It is generally diagnosed clinically after the irreversible loss of dopaminergic neurons and no general biomarkers currently exist. To gain insight into the underlying cellular causes of PD we aimed to quantify the proteomic differences between healthy control and PD patient cells.\nEXPERIMENTAL DESIGN: Sequential Window Acquisition of all THeoretical Mass Spectra was performed on primary cells from healthy controls and PD patients.\nRESULTS: In total, 1948 proteins were quantified and 228 proteins were significantly differentially expressed in PD patient cells. In PD patient cells, we identified seven significantly increased proteins involved in the unfolded protein response (UPR) and focused on cells with high and low amounts of PDIA6 and HYOU1. We discovered that PD patients with high amounts of PDIA6 and HYOU1 proteins were more sensitive to endoplasmic reticulum stress, in particular to tunicamycin. Data is available via ProteomeXchange with identifier PXD030723.\nCONCLUSIONS AND CLINICAL RELEVANCE: This data from primary patient cells has uncovered a critical role of the UPR in patients with PD and may provide insight to the underlying cellular dysfunctions in these patients.", "claims": [{"id": "claim-data-access", "statement": "Proteomic data is are freely available via ProteomeXchange with identifier PXD030723.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35579911", "locator": "sections[21] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "Proteomic data is are freely available via ProteomeXchange with identifier PXD030723."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SWATH-MS quantified 1,948 proteins, of which 228 had significantly different levels between PD and control cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35579911", "locator": "sections[10] \"Proteomic result summary\" paragraph 2", "quote": "A total of 1948 proteins were quantified using SWATH‐MS 1505 with two or more peptides."}, {"asset": "source:pmid:35579911", "locator": "sections[10] \"Proteomic result summary\" paragraph 2", "quote": "There were 228 proteins with significantly (ANOVA test) different levels when PD and controls were compared for proteins quantified with two, or more, peptides."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SWATH-MS quantified 1,948 proteins, of which 228 had significantly different levels between PD and control cells.", "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:35579911"], "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:PXD030723"], "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:PXD030723"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35579911", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/prca.202200015", "sha256": "sha256:a7e85f7a47c5b369736cf3ed0226e36659134b86c581505680887e3fa5c539f8", "bytes": 24650, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/prca.202200015", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9787017", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD030723", "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=PXD030723", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD030723", "version": null, "note": "Proteomic data is are freely available via ProteomeXchange with identifier PXD030723.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Proteomic data is are freely available via ProteomeXchange with identifier PXD030723.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic profiling of idiopathic Parkinson’s disease primary patient cells by SWATH-MS", "resolution_checked_at": "2026-11-01T18:06:51Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD030723 not downloaded", "asset:data:geo:PXD030723 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD030723"], "resolved_accessions": ["PXD030723"], "statements": ["Proteomic data is are freely available via ProteomeXchange with identifier PXD030723."], "basis": "The paper names PXD030723 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. 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