A method for whole protein isolation from human cranial bone.

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This has hindered the complete and accurate characterization of the human bone proteome thus far, leaving many bone-related disorders poorly understood. We sought to refine an existing method of protein extraction from mouse bone to extract whole proteins of varying molecular weights from human cranial bone. Whole protein was extracted from human cranial suture by mechanically processing samples using a method that limits protein degradation by minimizing heat introduction to proteins. The presence of whole protein was confirmed by western blotting. Mass spectrometry was used to sequence peptides and identify isolated proteins. The data have been deposited to the ProteomeXchange with identifier PXD003215. Extracted proteins were characterized as both intra- and extracellular and had molecular weights ranging from 9.4 to 629 kDa. High correlation scores among suture protein spectral counts support the reproducibility of the method. Ontology analytics revealed proteins of myriad functions including mediators of metabolic processes and cell organelles. These results demonstrate a reproducible method for isolation of whole protein from human cranial bone, representing a large range of molecular weights, origins and functions.", "claims": [{"id": "claim-target-result", "statement": "Correlation analysis of protein spectral counts showed high reproducibility among patent samples (>0.9), while fused sagittal samples showed >0.8 correlations and coronal-versus-other correlations were 0.6–0.7; the mass-spectrometry proteomics source data are available through ProteomeXchange via the PRIDE partner repository under dataset identifier PXD003215.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27677936", "locator": "sections[13] \"3.3 Method Reproducibility\" paragraph 2", "quote": "High correlation scores (>0.9) are observed when comparing patent samples even across patients and suture type (coronal, metopic), indicative of high experimental reproducibility."}, {"asset": "source:pmid:27677936", "locator": "sections[13] \"3.3 Method Reproducibility\" paragraph 2", "quote": "As shown, there is significant correlation among the fused sagittal samples (>0.8, indicated by large text in Figure 2B) and between sagittal and metopic samples. However, the correlation of protein spectral count between coronal and other types are however low (0.6-0.7, indicated by small text in Figure 2B)."}, {"asset": "source:pmid:27677936", "locator": "sections[8] \"2.6 Data analysis\" paragraph 3", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository17 with the dataset identifier PXD003215 and DOI 10.6019/PXD003215."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Correlation analysis of protein spectral counts showed high reproducibility among patent samples (>0.9), while fused sagittal samples showed >0.8 correlations and coronal-versus-other correlations were 0.6–0.7; the mass-spectrometry proteomics source data are available through ProteomeXchange via the PRIDE partner repository under dataset identifier PXD003215.", "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:27677936"], "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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