Rb interactome data and its modulations during cell cycle progression in HEK 293 cells.

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Despite its pertinent role in cell cycle regulation, comprehensive information on its interacting partners across cell cycle progression is lacking. Here, we aim to submit a comprehensive set of Rb interactors as the cell progresses from G0 through G1 and S into G2 phase in HEK 293 cell line. Affinity purification of HA-tagged Rb protein along with its interactors was analyzed by mass spectrometry (AP-MS). SILAC labeling enabled differentiation of Rb interactors in different cell cycle stages as well as their quantification - G0 cells were labeled with light labels of lysine and arginine (K0R0), cells in G1S transition were labeled with heavy labels (K8R10) while the G2 cells were labeled with medium labels (K6R6). LC-MS/MS analysis resulted in 6 wiff files which were submitted to protein pilot software for peptide identification and quantification. Here we submit the dataset which clearly captures the changing interacting partners of the Rb protein as the cell cycle progressed from G0 through G1S checkpoint into G2 phase. Data is publicly available via ProteomeXchange with identifier PXD007708.", "claims": [{"id": "claim-data-access", "statement": "Data is publicly available via ProteomeXchange with identifier PXD007708.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29552609", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data is publicly available via ProteomeXchange with identifier PXD007708."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used the ProteinPilot Paragon algorithm with a 1% accepted global false discovery rate, 95% minimum protein confidence, and PXD007708 as the source-data accession; its headline result was that the dataset captured changing Rb-interacting partners across the cell cycle.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29552609", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we submit the dataset which clearly captures the changing interacting partners of the Rb protein as the cell cycle progressed from G0 through G1S checkpoint into G2 phase."}, {"asset": "source:pmid:29552609", "locator": "sections[9] \"Data processing and analysis\" paragraph 2", "quote": "Protein pilot search was based on the paragon algorithm, a part of default statistics of the software."}, {"asset": "source:pmid:29552609", "locator": "sections[9] \"Data processing and analysis\" paragraph 2", "quote": "The threshold of 1% accepted Global False discovery rate from fit (G-FDR-fit) proteins"}, {"asset": "source:pmid:29552609", "locator": "sections[9] \"Data processing and analysis\" paragraph 2", "quote": "Minimum protein confidence threshold cutoff of 95%"}, {"asset": "source:pmid:29552609", "locator": "sections[9] \"Data processing and analysis\" paragraph 4", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [7] partner repository with the dataset identifier PXD007708."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used the ProteinPilot Paragon algorithm with a 1% accepted global false discovery rate, 95% minimum protein confidence, and PXD007708 as the source-data accession; its headline result was that the dataset captured changing Rb-interacting partners across the cell cycle.", "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:29552609"], "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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