Data in support of proteomic analysis of pneumococcal pediatric clinical isolates to construct a protein array.

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In addition, surface proteins can be the basis for serodiagnostic tools aiming at developing more affordable techniques for early diagnosis of infection in patients. We carried out a proteomic analysis of a collection of pediatric clinical isolates of Streptococcus pneumoniae, an important human pathogen responsible for more than 1.5 million child deaths worldwide. For that, cultured live bacterial cells were \"shaved\" with trypsin, and the recovered peptides were analyzed by LC/MS/MS. We selected 95 proteins to be produced as recombinant polypeptides, and printed them on an array. We probed the protein array with a collection of patient sera to define serodiagnostic antigens. The mass spectrometry proteomics data correspond to those published in [1] and have been deposited to the ProteomeXchange Consortium [2] via the PRIDE partner repository [3] with the dataset identifier PXD001740. The protein array raw data are provided as supplemental material in this article.", "claims": [{"id": "claim-data-access", "statement": "Data are available at the ProteomeXchange: PXD001740 and also provided as supplemental material within this article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26949725", "locator": "sections[1] \"Specification table\" paragraph 2", "quote": "Data are available at the ProteomeXchange: PXD001740 and also provided as supplemental material within this article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper identified potential serodiagnostic biomarkers by comparing patient and control seroresponses, using at least a 1.5-fold difference as the criterion; the raw protein-array reads are in Supplemental Dataset 1, processed IgG and IgM SMI values are in Tables S1 and S2, and the mass-spectrometry data are accessible through PRIDE under PXD001740.", "kind": "quantitative", "target": {"value": 1.5, "unit": "fold change", "tolerance": null, "source": "After comparison of the “patient” and “control” groups (see below in Section 3), the potential serodiagnostic biomarkers were defined as those with at least a 1.5-fold difference in seroresponse between both groups."}, "evidence": [{"asset": "source:pmid:26949725", "locator": "sections[5] \"Experimental design\" paragraph 2", "quote": "After comparison of the “patient” and “control” groups (see below in Section 3), the potential serodiagnostic biomarkers were defined as those with at least a 1.5-fold difference in seroresponse between both groups."}, {"asset": "source:pmid:26949725", "locator": "sections[3] \"Data\" paragraph 2", "quote": "Supplemental Dataset 1 contains all the raw protein array reads for patient and control sera, using both human anti-IgM and anti-IgG antibodies."}, {"asset": "source:pmid:26949725", "locator": "sections[3] \"Data\" paragraph 3", "quote": "Table S1 shows the processed data (mean±SD) of the IgG Signal Mean Intensity (SMI) values of all sera used in the protein array hybridization measurements."}, {"asset": "source:pmid:26949725", "locator": "sections[3] \"Data\" paragraph 4", "quote": "Table S2 shows the processed data (mean±SD) of the IgM Signal Mean Intensity (SMI) values of all sera used in the protein array hybridization measurements."}, {"asset": "source:pmid:26949725", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry proteomics data correspond to those published in [1] and have been deposited to the ProteomeXchange Consortium [2] via the PRIDE partner repository [3] with the dataset identifier PXD001740. 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The mass spectrometry proteomics data correspond to those published in [1] an", "lso known as pneumococcus, were subjected to proteomic analysis to identify the set of the most pro", "sera to define serodiagnostic antigens. The mass spectrometry proteomics data correspond to those publishe"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [".5 million child deaths worldwide. For that, cultured live bacterial cells were \"shaved\" with tryp", "bed in [6], consisting of “shaving” the live cultured cells with trypsin. Then, the fractions of p"], "order_basis": "paper_text_order:642", "id": "assay:2"}]}