A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33184295", "kind": "science-record", "revision": 7, "content_hash": "sha256:6aca121110c6f57edad0c6896af2f58bcbc77deddf298bc2da215d7f0a43c0ce", "created_at": "2026-11-01T15:41:15Z", "updated_at": "2026-11-01T22:02:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS.", "doi": "10.1038/s41597-020-00724-7", "pmid": "33184295", "authors": ["Mukul K Midha", "Ulrike Kusebauch", "David Shteynberg", "Charu Kapil", "Samuel L Bader", "Panga Jaipal Reddy", "David S Campbell", "Nitin S Baliga", "Robert L Moritz"], "journal": "Scientific data", "year": 2020, "abstract": "Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relies on spectral assay libraries that are generally derived from a priori measurements of peptides for each species. Although Escherichia coli (E. coli) is among the best studied model organisms, so far there is no spectral assay library for the bacterium publicly available. Here, we generated a spectral assay library for 4,014 of the 4,389 annotated E. coli proteins using one- and two-dimensional fractionated samples, and ion mobility separation enabling deep proteome coverage. We demonstrate the utility of this high-quality library with robustness in quantitation of the E. coli proteome and with rapid-chromatography to enhance throughput by targeted DIA-MS. The spectral assay library supports the detection and quantification of 91.5% of all E. coli proteins at high-confidence with 56,182 proteotypic peptides, making it a valuable resource for the scientific community. Data and spectral libraries are available via ProteomeXchange (PXD020761, PXD020785) and SWATHAtlas (SAL00222-28).", "claims": [{"id": "claim-method", "statement": "MAYU31 (version 1.07) was used to select an iProphet cutoff of 0.99617, resulting in a protein false discovery rate (FDR) of 1%.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33184295", "locator": "sections[12] \"Spectral and assay library generation\" paragraph 2", "quote": "MAYU31 (version 1.07) was used to select an iProphet cutoff of 0.99617, resulting in a protein false discovery rate (FDR) of 1%."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data and spectral libraries are available via ProteomeXchange (PXD020761, PXD020785) and SWATHAtlas (SAL00222-28).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33184295", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data and spectral libraries are available via ProteomeXchange (PXD020761, PXD020785) and SWATHAtlas (SAL00222-28)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33184295"], "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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