Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis.

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The findings are discussed in full in the research article \"Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis\" in Journal of Proteomics by Larsbrink et al. ([1], doi: 10.1016/j.jprot.2017.01.003). The bacterium was grown on three carbon sources (glucose, glucomannan, and galactomannan) which are likely to be nutrient sources or carbohydrate degradation products found in its natural habitat. The bacterium was grown on solid agarose plates to mimic the natural behaviour of growth on a solid surface. Secreted proteins were collected from the agarose following trypsin-mediated hydrolysis to peptides. The different carbon sources led to the secretion of different numbers and types of proteins. Most carbohydrate-degrading enzymes were found in the glucomannan-induced cultures. Several of these enzymes may have biotechnological potential in plant cell wall deconstruction for biofuel or biomaterial production, and several may have novel activities. A subset of carbohydrate-active enzymes (CAZymes) with predicted activities not obviously related to the growth substrates were also found in samples grown on each of the three carbohydrates. The full dataset is accessible at the PRIDE partner repository (ProteomeXchange Consortium) with the identifier PXD004305, and the full list of proteins detected is given in the supplementary material attached to this report.", "claims": [{"id": "claim-method", "statement": "Identification and quantification of proteins were performed using the MaxLFQ algorithm [9], searching against a database containing the full predicted proteome of C. pinensis, generated from the Uniprot database (7179 sequences in total) [10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28317006", "locator": "sections[12] \"Bioinformatics and statistical validation\" paragraph 2", "quote": "Identification and quantification of proteins were performed using the MaxLFQ algorithm [9], searching against a database containing the full predicted proteome of C. pinensis, generated from the Uniprot database (7179 sequences in total) [10]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is with the article and at PRIDE: PXD004305.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28317006", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Data is with the article and at PRIDE: PXD004305."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper analyzed the mass-spectrometry data with MaxQuant version 1.4.1.2 using the MaxLFQ algorithm, and the source data were deposited in PRIDE under dataset identifier PXD004305.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28317006", "locator": "sections[12] \"Bioinformatics and statistical validation\" paragraph 2", "quote": "The mass spectrometry data were analysed using MaxQuant [7], [8] version 1.4.1.2. 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