Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry.

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This neuropathologic form of α-syn contributes to PD progression and propagation of α-syn assemblies between neurons. The data we present here support the proteomic analysis used to identify neuronal proteins that specifically interact with extracellularly applied oligomeric or fibrillar α-syn assemblies (conditions 1 and 2, respectively) (doi: 10.15252/embj.201591397[1]). α-syn assemblies and their cellular partner proteins were pulled down from neuronal cell lysed shortly after exposure to exogenous α-syn assemblies and the associated proteins were identified by mass spectrometry using a shotgun proteomic-based approach. We also performed experiments on pure cultures of astrocytes to identify astrocyte-specific proteins interacting with oligomeric or fibrillar α-syn (conditions 3 and 4, respectively). For each condition, proteins interacting selectively with α-syn assemblies were identified by comparison to proteins pulled-down from untreated cells used as controls. The mass spectrometry data, the database search and the peak lists have been deposited to the ProteomeXchange Consortium database via the PRIDE partner repository with the dataset identifiers PRIDE: PXD002256 to PRIDE: PXD002263 and doi: 10.6019/PXD002256 to 10.6019/PXD002263.", "claims": [{"id": "claim-method", "statement": "Protein abundance was assessed by a label-free quantitative proteomic method using spectral counting.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26958642", "locator": "sections[5] \"Experimental design\" paragraph 2", "quote": "Protein abundance was assessed by a label-free quantitative proteomic method using spectral counting."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomic data (neurons and astrocytes) have been deposited to the ProteomeXchange Consortium [6] via the PRIDE partner repository with the dataset identifiers PXD002256 through PXD002263 and DOI 10.6019/PXD002256 through 10.6019/PXD002263.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26958642", "locator": "sections[11] \"Proteomic data deposition\" paragraph 2", "quote": "The mass spectrometry proteomic data (neurons and astrocytes) have been deposited to the ProteomeXchange Consortium [6] via the PRIDE partner repository with the dataset identifiers PXD002256 through PXD002263 and DOI 10.6019/PXD002256 through 10.6019/PXD002263."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:26958642"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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