A repository of assays to quantify 10,000 human proteins by SWATH-MS.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25977788", "kind": "science-record", "revision": 6, "content_hash": "sha256:cb3d6d9a37ce1d26a239fccdcda3ccf21938938b9364d2ec2b8ed6af6a3e3e3b", "created_at": "2026-11-01T15:40:08Z", "updated_at": "2026-11-01T21:20:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A repository of assays to quantify 10,000 human proteins by SWATH-MS.", "doi": "10.1038/sdata.2014.31", "pmid": "25977788", "authors": ["George Rosenberger", "Ching Chiek Koh", "Tiannan Guo", "Hannes L Röst", "Petri Kouvonen", "Ben C Collins", "Moritz Heusel", "Yansheng Liu", "Etienne Caron", "Anton Vichalkovski", "Marco Faini", "Olga T Schubert", "Pouya Faridi", "H Alexander Ebhardt", "Mariette Matondo", "Henry Lam", "Samuel L Bader", "David S Campbell", "Eric W Deutsch", "Robert L Moritz", "Stephen Tate", "Ruedi Aebersold"], "journal": "Scientific data", "year": 2014, "abstract": "Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).", "claims": [{"id": "claim-method", "statement": "False discovery rate (FDR) control was conducted using MAYU.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25977788", "locator": "sections[3] \"Sample overview\" paragraph 4", "quote": "False discovery rate (FDR) control was conducted using MAYU."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25977788", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using MAYU-based statistical filtering, the study produced a combined human SWATH-MS assay library for more than 10,000 proteins, covering 50.9% of UniProtKB/Swiss-Prot proteins; the source data are available through ProteomeXchange (PXD000953–954) and SWATHAtlas (SAL00016–35).", "kind": "quantitative", "target": {"value": 50.9, "unit": "per cent", "tolerance": null, "source": "This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research."}, "evidence": [{"asset": "source:pmid:25977788", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens."}, {"asset": "source:pmid:25977788", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research."}, {"asset": "source:pmid:25977788", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using MAYU-based statistical filtering, the study produced a combined human SWATH-MS assay library for more than 10,000 proteins, covering 50.9% of UniProtKB/Swiss-Prot proteins; the source data are available through ProteomeXchange (PXD000953–954) and SWATHAtlas (SAL00016–35).", "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:25977788"], "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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The combined assay library is provided with all target and decoy assays, but only proteotypic assays were considered for all downstream analysis.", "", ""], ["Proteins", "10,316", "11,588"], ["Peptides", "139,449", "146,576"], ["Precursors", "194,052", "204,545"], ["Transitions", "1,164,312", "1,227,270"]], "row_count": 6, "column_count": 3, "numeric_cells": 9, "header_rows": 1, "locator": "section[28]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:25977788:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:72cccbc69088f279bba68b9d13b5185a5d12a1330995173153869da624149fad", "bytes": 1331, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[29]/table-wrap[1]#t3", "version": null, "note": "Identification statistics of the combined and sample-specific assay libraries.", "structure": {"pmcid": "PMC4322573", "section_index": 29, "section_title": "Applicability of the combined assay library for SWATH-MS targeted data analysis", "row_count": 9, "column_count": 9}, "table": {"label": "Table 3", "caption": "Identification statistics of the combined and sample-specific assay libraries.", "rows": [["Protein FDR", "CAL HeLa", "", "ss HeLa", "CAL U2OS", "ss U2OS"], ["", "prot", "pep", "prot", "pep", "prot", "pep", "prot", "pep"], ["The number of identified proteotypic peptides and proteins in SWATH-MS datasets of whole cell lysates of HeLa and U2OS cell lines at commonly used protein FDR cutoffs using combined (CAL) and sample-specific (ss) assay libraries is reported. 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The true positive protein (prot) and peptide (pep) identifications for the combined assay library and sample-specific assay libraries are reported as estimated by MAYU.", "", "", "", "", "", "", "", ""], ["1%", "2,417", "14,930", "2,353", "14,635", "2,617", "15,608", "2,452", "14,360"], ["2%", "2,730", "17,294", "2,467", "15,416", "2,989", "18,321", "2,541", "14,982"], ["5%", "3,246", "21,128", "2,514", "15,672", "3,486", "21,893", "2,552", "15,003"], ["NS 1%", "2,608", "23,075", "1,750", "14,999", "2,803", "24,009", "1,763", "14,599"], ["NS 2%", "2,804", "25,005", "1,798", "15,537", "2,965", "25,497", "1,815", "15,002"], ["NS 5%", "3,111", "28,002", "1,820", "15,668", "3,241", "28,442", "1,819", "14,999"]], "row_count": 9, "column_count": 9, "numeric_cells": 54, "header_rows": 2, "locator": "section[29]/table-wrap[1]#t3"}}], "gaps": ["asset:data:geo:PXD000953 not downloaded", "asset:data:geo:PXD000953 licence not read", "asset:data:geo:PXD000954 not downloaded", "asset:data:geo:PXD000954 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "MAYU", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "False discovery rate (FDR) control was conducted using MAYU."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 50.9, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. 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