Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26425664", "kind": "science-record", "revision": 8, "content_hash": "sha256:061845af76400144d7106924e66f479027d1f3c100e53c14572c82eb30c3cf41", "created_at": "2026-11-01T15:40:11Z", "updated_at": "2026-11-01T22:42:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells.", "doi": "10.1016/j.dib.2015.08.010", "pmid": "26425664", "authors": ["Samuel Rogers", "Rachael A McCloy", "Benjamin L Parker", "Rima Chaudhuri", "Velimir Gayevskiy", "Nolan J Hoffman", "D Neil Watkins", "Roger J Daly", "David E James", "Andrew Burgess"], "journal": "Data in brief", "year": 2015, "abstract": "The presence or absence of a phosphorylation on a substrate at any particular point in time is a functional readout of the balance in activity between the regulatory kinase and the counteracting phosphatase. Understanding how stable or short-lived a phosphorylation site is required for fully appreciating the biological consequences of the phosphorylation. Our current understanding of kinases and their substrates is well established; however, the role phosphatases play is less understood. Therefore, we utilized a phosphatase dependent model of mitotic exit to identify potential substrates that are preferentially dephosphorylated. Using this method, we identified >16,000 phosphosites on >3300 unique proteins, and quantified the temporal phosphorylation changes that occur during early mitotic exit (McCloy et al., 2015 [1]). Furthermore, we annotated the majority of these phosphorylation sites with a high confidence upstream kinase using published, motif and prediction based methods. The results from this study have been deposited into the ProteomeXchange repository with identifier PXD001559. Here we provide additional analysis of this dataset; for each of the major mitotic kinases we identified motifs that correlated strongly with phosphorylation status. These motifs could be used to predict the stability of phosphorylated residues in proteins of interest, and help infer potential functional roles for uncharacterized phosphorylations. In addition, we provide validation at the single cell level that serine residues phosphorylated by Cdk are stable during phosphatase dependent mitotic exit. In summary, this unique dataset contains information on the temporal mitotic stability of thousands of phosphorylation sites regulated by dozens of kinases, and information on the potential preference that phosphatases have at both the protein and individual phosphosite level. The compellation of this data provides an invaluable resource for the wider research community.", "claims": [{"id": "claim-method", "statement": "A moderated t-test was used to identify phosphosites that are significantly up or down-regulated using Linear Models for Microarray and RNA-Seq Data (LIMMA) package in R [9].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26425664", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "A moderated t-test was used to identify phosphosites that are significantly up or down-regulated using Linear Models for Microarray and RNA-Seq Data (LIMMA) package in R [9]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We have uploaded all the raw mass spectrometry data files and MaxQuant output files necessary to reanalyze the complete dataset to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [7] with the identifier PXD001559. Annotated spectra can be viewed using the free MS-viewer [8] (http://prospector2.ucsf.edu) with the search key gsmtp1s5q7. In addition, a summary of this data, in an easy to use excel spreadsheet, is provided with this manuscript (Supplementary Table S1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26425664", "locator": "sections[11] \"Description of dataset contained on public repositories\" paragraph 2", "quote": "We have uploaded all the raw mass spectrometry data files and MaxQuant output files necessary to reanalyze the complete dataset to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [7] with the identifier PXD001559. Annotated spectra can be viewed using the free MS-viewer [8] (http://prospector2.ucsf.edu) with the search key gsmtp1s5q7. In addition, a summary of this data, in an easy to use excel spreadsheet, is provided with this manuscript (Supplementary Table S1)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used a moderated t-test with LIMMA, followed by Benjamini–Hochberg correction, and deposited the raw mass spectrometry and MaxQuant source data in the PRIDE repository under identifier PXD001559.", "kind": "quantitative", "target": {"value": 5.0, "unit": "per cent", "tolerance": null, "source": "Identified sites were then corrected for multiple hypothesis testing using the Benjamini and Hochberg method (controlling for 5% false discovery rate)."}, "evidence": [{"asset": "source:pmid:26425664", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "A moderated t-test was used to identify phosphosites that are significantly up or down-regulated using Linear Models for Microarray and RNA-Seq Data (LIMMA) package in R [9]."}, {"asset": "source:pmid:26425664", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "Identified sites were then corrected for multiple hypothesis testing using the Benjamini and Hochberg method (controlling for 5% false discovery rate)."}, {"asset": "source:pmid:26425664", "locator": "sections[11] \"Description of dataset contained on public repositories\" paragraph 2", "quote": "We have uploaded all the raw mass spectrometry data files and MaxQuant output files necessary to reanalyze the complete dataset to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [7] with the identifier PXD001559."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used a moderated t-test with LIMMA, followed by Benjamini–Hochberg correction, and deposited the raw mass spectrometry and MaxQuant source data in the PRIDE repository under identifier PXD001559.", "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:26425664"], "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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