Quantitative proteomics of rat and human pancreatic beta cells.

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The mass spectrometry data of the human and rat pancreatic beta cells and the resulting proteome search output from ProteinLynx GlobalSERVER (PLGS) have been deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository with the dataset identifiers PXD001539 (human) and PXD001816 (rat). From these mass spectrometry data, 'relative molar amount units' between cell types and across species were calculated. Biological relevance: These data provide a quantitative view on the unfractionated proteomes of human and rat beta and alpha cells. It is likely biased towards the proteins with higher molar abundance, relating to core functional pathways, but also includes several proteins with an islet-enriched expression. The quality of the cell preps is state-of-the-art, and the label-free quantitation is both precise and accurate, allowing detailed quantitative analysis.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry data of the human and rat pancreatic beta cells and the resulting proteome search output from ProteinLynx GlobalSERVER (PLGS) have been deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository with the dataset identifiers PXD001539 (human) and PXD001816 (rat).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26217750", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mass spectrometry data of the human and rat pancreatic beta cells and the resulting proteome search output from ProteinLynx GlobalSERVER (PLGS) have been deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository with the dataset identifiers PXD001539 (human) and PXD001816 (rat)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports highly reproducible label-free alternate-scanning LC-MS/MS protein quantification with overall technical plus biological imprecision below 20%, using geometric normalization for cross-cell-type and cross-species comparisons; the source data were deposited through ProteomeXchange/PRIDE as PXD001539 for human samples and PXD001816 for rat samples.", "kind": "quantitative", "target": {"value": 20.0, "unit": "per cent", "tolerance": null, "source": "We showed that alternate-scanning LC-MS/MS generated highly reproducible protein quantifications (with overall technical plus biological imprecision<20% and high accuracies as judged by correct measurement of multi-enzyme stoichiometry [4])."}, "evidence": [{"asset": "source:pmid:26217750", "locator": "sections[2] \"Value of the data\" paragraph 2", "quote": "We showed that alternate-scanning LC-MS/MS generated highly reproducible protein quantifications (with overall technical plus biological imprecision<20% and high accuracies as judged by correct measurement of multi-enzyme stoichiometry [4])."}, {"asset": "source:pmid:26217750", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mass spectrometry data of the human and rat pancreatic beta cells and the resulting proteome search output from ProteinLynx GlobalSERVER (PLGS) have been deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository with the dataset identifiers PXD001539 (human) and PXD001816 (rat)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reports highly reproducible label-free alternate-scanning LC-MS/MS protein quantification with overall technical plus biological imprecision below 20%, using geometric normalization for cross-cell-type and cross-species comparisons; the source data were deposited through ProteomeXchange/PRIDE as PXD001539 for human samples and PXD001816 for rat samples.", "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:26217750"], "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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