The proteome of mouse vestibular hair bundles over development.

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To understand how the protein composition of the bundle changes during development, we isolated bundles from young (postnatal days P4-P6) and mature (P21-P25) mouse utricles using the twist-off method, then characterized their constituent proteins using liquid-chromatography tandem mass spectrometry with data-dependent acquisition. Using MaxQuant and label-free quantitation, we measured relative abundances of proteins in both bundles and in the whole utricle; comparison of protein abundance between the two fractions allows calculation of enrichment in bundles. These data, which are available via ProteomeXchange with identifier PXD002167, will be useful for examining the proteins present in mammalian vestibular bundles and how their concentrations change over development.", "claims": [{"id": "claim-method", "statement": "Similarly, principal component analysis showed that each of the four sets of samples were clearly distinguished from each other (Fig. 2c,d).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26401315", "locator": "sections[14] \"Comparison of biological replicates for each condition\" paragraph 2", "quote": "Similarly, principal component analysis showed that each of the four sets of samples were clearly distinguished from each other (Fig. 2c,d)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data and analysis files, described below, have been deposited to the ProteomeXchange repository (accession number PXD002167; http://www.proteomexchange.org).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26401315", "locator": "sections[11] \"Data Records\" paragraph 2", "quote": "All data and analysis files, described below, have been deposited to the ProteomeXchange repository (accession number PXD002167; http://www.proteomexchange.org)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used principal component analysis and pairwise Pearson correlations to assess replicate similarity and distinguish developmental and sample conditions; the source data are available through ProteomeXchange under identifier PXD002167.", "kind": "quantitative", "target": {"value": 90.0, "unit": "per cent", "tolerance": null, "source": "Similarly, principal component analysis showed that each of the four sets of samples were clearly distinguished from each other (Fig. 2c,d). Over 90% of the variance was accounted for by PC1."}, "evidence": [{"asset": "source:pmid:26401315", "locator": "sections[14] \"Comparison of biological replicates for each condition\" paragraph 2", "quote": "Similarly, principal component analysis showed that each of the four sets of samples were clearly distinguished from each other (Fig. 2c,d). Over 90% of the variance was accounted for by PC1."}, {"asset": "source:pmid:26401315", "locator": "sections[14] \"Comparison of biological replicates for each condition\" paragraph 2", "quote": "Note that the biological replicate samples showed highest Pearson correlation coefficients (numbers in boxes)."}, {"asset": "source:pmid:26401315", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These data, which are available via ProteomeXchange with identifier PXD002167, will be useful for examining the proteins present in mammalian vestibular bundles and how their concentrations change over development."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used principal component analysis and pairwise Pearson correlations to assess replicate similarity and distinguish developmental and sample conditions; the source data are available through ProteomeXchange under identifier PXD002167.", "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:26401315"], "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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Using MaxQu", "ow for bundle isolation, sample preparation, mass spectrometry, and data analysis is shown in Fig. 1c. Info", "Supplementary Table 1. Samples analysed for mass spectrometry. Sample preparation Hair bundles were purifi", "tubes. Bundle samples were later pooled for mass spectrometry analysis. For analysis of whole utricular ma"], "order_basis": "paper_text_order:502", "id": "assay:2"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Similarly, principal component analysis showed that each of the four sets of samples were clearly distinguished from each other (Fig. 2c,d)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}