Proteome data to explore the impact of pBClin15 on Bacillus cereus ATCC 14579.

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We report all the peptides and proteins identified and quantified in B. cereus with and without pBClin15. Proteins were classified into functional groups using the information available in the KEGG classification and we reported their abundance in term of normalized spectral abundance factor. The repertoire of experimentally confirmed proteins of B. cereus presented here is the largest ever reported, and provides new insights into the interplay between pBClin15 and its host B. cereus ATCC 14579. The data reported here is related to a published shotgun proteomics analysis regarding the role of pBClin15, \"Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics\" Madeira et al. [1]. All the associated mass spectrometry data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (http://www.ebi.ac.uk/pride/), with the dataset identifier PRIDE: PXD001568, PRIDE: PXD002788 and PRIDE: PXD002789.", "claims": [{"id": "claim-method", "statement": "Analyses of abundance level change of proteins were performed with the LIMMA package by the LIMMA Voom method [12]. The data were normalized with the trimmed mean of M-values (TMM) normalization. Then, quantitative proteomics data were analyzed by empirical Bayes moderation of the standard errors towards a common value.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27547804", "locator": "sections[9] \"Data analysis\" paragraph 2", "quote": "Analyses of abundance level change of proteins were performed with the LIMMA package by the LIMMA Voom method [12]. 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[1]. All the associated mass spectrometry data have been deposited in the ProteomeXcha", "rrows. Sample preparation and shotgun tandem mass spectrometry Soluble proteins were extracted and processe", "e resulting peptides were analyzed by tandem mass spectrometry as described previously [5], [9]. The peptid", "orted here is related to a published shotgun proteomics analysis regarding the role of pBClin15, \"De"], "order_basis": "paper_text_order:770", "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": ["s (with and without pBClin15, [3], [4]) were cultured in batches as described previously [5] with thr", "l strain, ATCC 14,579 (WT). The strains were cultured in MOD medium supplemented with 30 mM glucose u"], "order_basis": "paper_text_order:1374", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Analyses of abundance level change of proteins were performed with the LIMMA package by the LIMMA Voom method [12]. The data were normalized with the trimmed mean of M-values (TMM) normalization. Then, quantitative proteomics data were analyzed by empirical Bayes moderation of the standard errors towards a common value."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}