Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34433823", "kind": "science-record", "revision": 6, "content_hash": "sha256:f84de99fbe605a818f02ddb09cb8aef80677dcdf7cbb496ce891301874ab239e", "created_at": "2026-11-01T15:41:49Z", "updated_at": "2026-11-01T21:26:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds.", "doi": "10.1038/s41597-021-01008-4", "pmid": "34433823", "authors": ["Deborah O Dele-Oni", "Karen E Christianson", "Shawn B Egri", "Alvaro Sebastian Vaca Jacome", "Katherine C DeRuff", "James Mullahoo", "Vagisha Sharma", "Desiree Davison", "Tak Ko", "Michael Bula", "Joel Blanchard", "Jennie Z Young", "Lev Litichevskiy", "Xiaodong Lu", "Daniel Lam", "Jacob K Asiedu", "Caidin Toder", "Adam Officer", "Ryan Peckner", "Michael J MacCoss", "Li-Huei Tsai", "Steven A Carr", "Malvina Papanastasiou", "Jacob D Jaffe"], "journal": "Scientific data", "year": 2021, "abstract": "While gene expression profiling has traditionally been the method of choice for large-scale perturbational profiling studies, proteomics has emerged as an effective tool in this context for directly monitoring cellular responses to perturbations. We previously reported a pilot library containing 3400 profiles of multiple perturbations across diverse cellular backgrounds in the reduced-representation phosphoproteome (P100) and chromatin space (Global Chromatin Profiling, GCP). Here, we expand our original dataset to include profiles from a new set of cardiotoxic compounds and from astrocytes, an additional neural cell model, totaling 5300 proteomic signatures. We describe filtering criteria and quality control metrics used to assess and validate the technical quality and reproducibility of our data. To demonstrate the power of the library, we present two case studies where data is queried using the concept of \"connectivity\" to obtain biological insight. All data presented in this study have been deposited to the ProteomeXchange Consortium with identifiers PXD017458 (P100) and PXD017459 (GCP) and can be queried at https://clue.io/proteomics .", "claims": [{"id": "claim-method", "statement": "We further tested reproducibility by performing 10 random permutation tests of all samples compared with the permutation null and investigated whether true replicate correlations were at the highest 5% of a distribution (q value < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34433823", "locator": "sections[8] \"Technical Validation\" paragraph 7", "quote": "We further tested reproducibility by performing 10 random permutation tests of all samples compared with the permutation null and investigated whether true replicate correlations were at the highest 5% of a distribution (q value < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All MS raw files, Skyline documents, and processed GCT files (Levels 0-4 data) are publicly available on Panorama Public42 for P10043 and GCP44 (Supplementary Table 2). These data were deposited to the ProteomeXchange Consortium via Panorama Public45 with identifiers PXD017458 (P100) and PXD017459 (GCP). The data can also be found in the LINCS Data Portal with identifiers LDS-41234 (“P100 aggregated data - Chemical perturbations”) and LDS-41235 (“GCP aggregated data - Chemical perturbations”). Connectivity scores (Level 5 data) can be explored and queried using Touchstone-P, part of the Proteomics Connectivity Hub, available at https://clue.io/proteomics.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34433823", "locator": "sections[7] \"Data Records\" paragraph 2", "quote": "All MS raw files, Skyline documents, and processed GCT files (Levels 0-4 data) are publicly available on Panorama Public42 for P10043 and GCP44 (Supplementary Table 2). These data were deposited to the ProteomeXchange Consortium via Panorama Public45 with identifiers PXD017458 (P100) and PXD017459 (GCP). 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Briefly, A375, A549, and YAPC cells were cultured in RPMI 1640 medium (Thermo Fisher Scientific),", "(Thermo Fisher Scientific), MCF7 cells were cultured in DMEM (Thermo Fisher Scientific), and PC3 cel", "hermo Fisher Scientific), and PC3 cells were cultured in RPMI 1640 medium containing 1 mM sodium pyru", "431542 (Tocris Bioscience). Astrocytes were cultured in astrocyte medium (ScienCell, Cat No. 1801)."], "order_basis": "paper_text_order:1255", "id": "assay:1"}]}