Identification of Drosophila centromere associated proteins by quantitative affinity purification-mass spectrometry.

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CENP-A(CID) builds the foundation for the assembly of a large network of proteins. In contrast to mammalian systems, the protein composition of Drosophila centromeres has not been comprehensively investigated. Here we describe the proteome of Drosophila melanogaster centromeres as analyzed by quantitative affinity purification-mass spectrometry (AP-MS). The AP-MS input chromatin material was prepared from D. melanogaster cell lines expressing CENP-A(CID) or H3.3 fused to EGFP as baits. Centromere chromatin enriched proteins were identified based on their relative abundance in CENP-A(CID)-GFP compared to H3.3-GFP or mock affinity-purifications. The analysis yielded 86 proteins specifically enriched in centromere chromatin preparations. The data accompanying the manuscript on this approach (Barth et al., 2015, Proteomics 14:2167-78, DOI: 10.1002/pmic.201400052) has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000758.", "claims": [{"id": "claim-method", "statement": "ANOVA was applied in DanteR (vs 0.2, PNNL, Richland, WA, USA) [6] to calculate protein enrichment factors and p-values and obtained p-values were corrected for multiple hypothesis testing by the Benjamini–Hochberg method [7].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26306323", "locator": "sections[9] \"Protein identification and statistical analysis\" paragraph 3", "quote": "ANOVA was applied in DanteR (vs 0.2, PNNL, Richland, WA, USA) [6] to calculate protein enrichment factors and p-values and obtained p-values were corrected for multiple hypothesis testing by the Benjamini–Hochberg method [7]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data accompanying the manuscript on this approach (Barth et al., 2015, Proteomics 14:2167-78, DOI: 10.1002/pmic.201400052) has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000758.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26306323", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The data accompanying the manuscript on this approach (Barth et al., 2015, Proteomics 14:2167-78, DOI: 10.1002/pmic.201400052) has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000758."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis yielded 86 proteins specifically enriched in centromere chromatin preparations.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26306323", "locator": "sections[9] \"Protein identification and statistical analysis\" paragraph 3", "quote": "ANOVA was applied in DanteR (vs 0.2, PNNL, Richland, WA, USA) [6] to calculate protein enrichment factors and p-values and obtained p-values were corrected for multiple hypothesis testing by the Benjamini–Hochberg method [7]."}, {"asset": "source:pmid:26306323", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The data accompanying the manuscript on this approach (Barth et al., 2015, Proteomics 14:2167-78, DOI: 10.1002/pmic.201400052) has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000758."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis yielded 86 proteins specifically enriched in centromere chromatin preparations.", "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:26306323"], "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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