Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis.

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Despite recent advances in antimicrobial therapy, pneumococcal meningitis remains a life-threatening disease. Furthermore, long-term sequelae are a major concern for survivors. Hence, a better understanding of the processes occurring in the central nervous system is crucial to the development of more effective management strategies. We used mass spectrometry based quantitative proteomics to identify protein changes in cerebrospinal fluid from children with Streptococcus pneumoniae infection, compared with children admitted to hospital with bacterial meningitis symptoms but negative diagnosis. Samples were analysed, by label free proteomics, in two independent cohorts (cohort 1: cases (n = 8) and hospital controls (n = 4); cohort 2: cases (n = 8), hospital controls (n = 8)). Over 200 human proteins were differentially expressed in each cohort, of which 65% were common to both. Proteins involved in the immune response and exosome signalling were significantly enriched in the infected samples. For a subset of proteins derived from the proteome analysis, we corroborated the proteomics data in a third cohort (hospital controls (n = 15), healthy controls (n = 5), cases (n = 20)) by automated quantitative western blotting, with excellent agreement with our proteomics findings. Proteomics data are available via ProteomeXchange with identifier PXD004219.", "claims": [{"id": "claim-method", "statement": "Probabilities were calculated using the t-test function in R and corrected for multiple testing by Benjamini and Hochberg method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28765563", "locator": "sections[4] \"Label-free quantification of CSF proteins\" paragraph 5", "quote": "Probabilities were calculated using the t-test function in R and corrected for multiple testing by Benjamini and Hochberg method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE54 partner repository with the dataset identifier PXD004219 and 10.6019/PXD004219.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28765563", "locator": "sections[11] \"Database search parameters and acceptance criteria for identification\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE54 partner repository with the dataset identifier PXD004219 and 10.6019/PXD004219."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Label-free quantitative proteomics identified over 200 differentially expressed human proteins in each cohort, with 65% common to both, using peptide-level filtering at a 1% false discovery rate; the source proteomics data are available through ProteomeXchange under identifier PXD004219.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28765563", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Samples were analysed, by label free proteomics, in two independent cohorts (cohort 1: cases (n = 8) and hospital controls (n = 4); cohort 2: cases (n = 8), hospital controls (n = 8))."}, {"asset": "source:pmid:28765563", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Over 200 human proteins were differentially expressed in each cohort, of which 65% were common to both."}, {"asset": "source:pmid:28765563", "locator": "sections[3] \"Identification of CSF proteins\" paragraph 2", "quote": "To ensure confidence in proteins listed here, we adopted a rigorous filtering criterion, restricting the protein list to those that were identified with at least two unique peptides after applying a 1% FDR at the peptide level."}, {"asset": "source:pmid:28765563", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Proteomics data are available via ProteomeXchange with identifier PXD004219."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Label-free quantitative proteomics identified over 200 differentially expressed human proteins in each cohort, with 65% common to both, using peptide-level filtering at a 1% false discovery rate; the source proteomics data are available through ProteomeXchange under identifier PXD004219.", "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:28765563"], "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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