Hair-bundle proteomes of avian and mammalian inner-ear utricles.

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We report here proteomes of inner-ear hair bundles from three species (chick, mouse, and rat), which were collected on LTQ or LTQ Velos ion-trap mass spectrometers; the constituent proteins were quantified using MS2 intensities, which are the summed intensities of all peptide fragmentation spectra matched to a protein. The data are available via ProteomeXchange with identifiers PXD002410 (chick LTQ), PXD002414 (chick Velos), PXD002415 (mouse Velos), and PXD002416 (rat LTQ). The two chick bundle datasets compared favourably to a third, already-described chick bundle dataset, which was quantified using MS1 peak intensities, the summed intensities of peptides identified by high-resolution mass spectrometry (PXD000104; updated analysis in PXD002445). The mouse bundle dataset described here was comparable to a different mouse bundle dataset quantified using MS1 intensities (PXD002167). These six datasets will be useful for identifying the core proteome of vestibular hair bundles.", "claims": [{"id": "claim-method", "statement": "Principal component analysis showed that for each dataset, the bundle and utricle samples were clearly distinguished from each other", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26645194", "locator": "sections[23] \"Comparison of biological replicates for each condition\" paragraph 2", "quote": "Principal component analysis showed that for each dataset, the bundle and utricle samples were clearly distinguished from each other"}], "state": "complete"}, {"id": "claim-data-access", "statement": "Complete search results are located in the ProteomeXchange datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26645194", "locator": "sections[11] \"Protein assembly by PAW\" paragraph 5", "quote": "Complete search results are located in the ProteomeXchange datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:26645194"], "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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N/A, not applicable.", "", "", "", ""], ["Chick_LTQ", "Chick_LTQ_BUN", "3±1%", "2.8%", "9.4%"], ["Chick_LTQ", "Chick_LTQ_UTR", "N/A", "5.7%", "0.9%"], ["Chick_Velos", "Chick_Velos_BUN", "6±2%", "2.3%", "11.3%"], ["Chick_Velos", "Chick_Velos_UTR", "N/A", "0.6%", "5.2%"], ["Chick_Orbitrap", "Chick_Orbitrap_BUN", "18±12%", "N/A", "4.6%"], ["Chick_Orbitrap", "Chick_Orbitrap_UTR", "N/A", "N/A", "4.6%"], ["Rat_LTQ", "Rat_LTQ_BUN", "35±14%", "2.6%", "2.8%"], ["Rat_LTQ", "Rat_LTQ_UTR", "N/A", "1.0%", "2.5%"], ["Mouse_Velos", "Mouse_Velos_BUN", "5±7%", "15%", "1.3%"], ["Mouse_Velos", "Mouse_Velos_UTR", "N/A", "2.0%", "1.1%"], ["Mouse_Orbitrap_P23", "Mouse_Orbitrap_P23_BUN", "16±11%", "N/A", "2.6%"], ["Mouse_Orbitrap_P23", "Mouse_Orbitrap_P23_UTR", "N/A", "N/A", "1.1%"]], "row_count": 14, "column_count": 5, "numeric_cells": 31, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t2"}}], "gaps": ["asset:data:geo:PXD002445 not downloaded", "asset:data:geo:PXD002445 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Principal component analysis showed that for each dataset, the bundle and utricle samples were clearly distinguished from each other"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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The two chi", "D000104; updated analysis in PXD002445). The mouse bundle dataset described here was comparable", "described here was comparable to a different mouse bundle dataset quantified using MS1 intensit"], "order_basis": "paper_text_order:221", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["es of peptides identified by high-resolution mass spectrometry (PXD000104; updated analysis in PXD002445).", "ow for bundle isolation, sample preparation, mass spectrometry, and data analysis is shown in Fig. 1. Infor", ".(a) Sample and data processing workflow for mass spectrometry analysis. (b) Sample groups. 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