Data from quantitative label free proteomics analysis of rat spleen.

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A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.", "claims": [{"id": "claim-method", "statement": "One-way ANOVA was used to calculate the p-value based on the transformed values.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27358910", "locator": "sections[10] \"Data analysis\" paragraph 3", "quote": "One-way ANOVA was used to calculate the p-value based on the transformed values."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available from ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) [5] PRIDE: PXD003520; Project Name: Rat spleen proteomics profiling Project accession: PXD003520; Project DOI:10.6019/PXD003520; Reviewer account details: Username: reviewer67804@ebi.ac.uk; Password: tyP0Zh1t.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27358910", "locator": "sections[11] \"Data availability\" paragraph 2", "quote": "Data are available from ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) [5] PRIDE: PXD003520; Project Name: Rat spleen proteomics profiling Project accession: PXD003520; Project DOI:10.6019/PXD003520; Reviewer account details: Username: reviewer67804@ebi.ac.uk; Password: tyP0Zh1t."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 3,484 different rat spleen proteins in total, using one-way ANOVA for statistical analysis and providing the underlying Progenesis output in Supplementary information 3.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27358910", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides)."}, {"asset": "source:pmid:27358910", "locator": "sections[10] \"Data analysis\" paragraph 3", "quote": "One-way ANOVA was used to calculate the p-value based on the transformed values."}, {"asset": "source:pmid:27358910", "locator": "sections[10] \"Data analysis\" paragraph 3", "quote": "Dataset of the Progenesis analysis is shown in Supplementary information 3."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 3,484 different rat spleen proteins in total, using one-way ANOVA for statistical analysis and providing the underlying Progenesis output in Supplementary information 3.", "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:27358910"], "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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