{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T04:07:52Z","timestamp":1777608472767,"version":"3.51.4"},"reference-count":14,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2020,11,27]],"date-time":"2020-11-27T00:00:00Z","timestamp":1606435200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Data"],"abstract":"<jats:p>Here we provide all datasets and details applied in the construction of a composite protein database required for the proteogenomic analyses of the article \u201cPutative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database\u201d. All data, subdivided into six datasets, are deposited at the Mendeley Data repository as follows. Dataset_1 provides our composite database \u201cAll_Databases_5950827_sequences.fasta\u201d derived from six smaller databases composed of (i) protein sequences retrieved from public databases related to cephalopods\u2019 salivary glands, (ii) proteins identified with Proteome Discoverer software using our original data obtained by shotgun proteomic analyses of posterior salivary glands (PSGs) from three Octopus vulgaris specimens (provided as Dataset_2) and (iii) a non-redundant antimicrobial peptide (AMP) database. Dataset_3 includes the transcripts obtained by de novo assembly of 16 transcriptomes from cephalopods\u2019 PSGs using CLC Genomics Workbench. Dataset_4 provides the proteins predicted by the TransDecoder tool from the de novo assembly of 16 transcriptomes of cephalopods\u2019 PSGs. Further details about database construction, as well as the scripts and command lines used to construct them, are deposited within Dataset_5 and Dataset_6. The data provided in this article will assist in unravelling the role of cephalopods\u2019 PSGs in feeding strategies, toxins and AMP production.<\/jats:p>","DOI":"10.3390\/data5040110","type":"journal-article","created":{"date-parts":[[2020,11,27]],"date-time":"2020-11-27T09:16:49Z","timestamp":1606468609000},"page":"110","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Data Employed in the Construction of a Composite Protein Database for Proteogenomic Analyses of Cephalopods Salivary Apparatus"],"prefix":"10.3390","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9874-933X","authenticated-orcid":false,"given":"Daniela","family":"Almeida","sequence":"first","affiliation":[{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5211-972X","authenticated-orcid":false,"given":"Dany","family":"Dom\u00ednguez-P\u00e9rez","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"}]},{"given":"Ana","family":"Matos","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"},{"name":"Biology Department of the Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9908-2418","authenticated-orcid":false,"given":"Guillermin","family":"Ag\u00fcero-Chapin","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"},{"name":"Biology Department of the Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6155-5083","authenticated-orcid":false,"given":"Yuselis","family":"Casta\u00f1o","sequence":"additional","affiliation":[{"name":"BioMark Sensor Research, Instituto Superior de Engenharia do Porto, 4200-072 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3585-2417","authenticated-orcid":false,"given":"Vitor","family":"Vasconcelos","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"},{"name":"Biology Department of the Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"}]},{"given":"Alexandre","family":"Campos","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1328-1732","authenticated-orcid":false,"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"},{"name":"Biology Department of the Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2020,11,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Almeida, D., Dom\u00ednguez-P\u00e9rez, D., Matos, A., Ag\u00fcero-Chapin, G., Os\u00f3rio, H., Vasconcelos, V., Campos, A., and Antunes, A. (2020). Putative antimicrobial peptides of the posterior salivary glands from the cephalopod Octopus vulgaris revealed by exploring a composite protein database. Antibiotics, 9.","DOI":"10.3390\/antibiotics9110757"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3866","DOI":"10.1021\/acs.jproteome.8b00525","article-title":"Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common Octopus Octopus vulgaris","volume":"17","author":"Fingerhut","year":"2018","journal-title":"J. Proteome Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2553","DOI":"10.1093\/bioinformatics\/btv180","article-title":"Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences","volume":"31","author":"Salgado","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_4","unstructured":"(2019, April 14). Proteomics Toolkit (Protk). Available online: https:\/\/github.com\/iracooke\/protk."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/nmeth.1322","article-title":"Universal sample preparation method for proteome analysis","volume":"6","author":"Zougman","year":"2009","journal-title":"Nat. Methods"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: A worldwide hub of protein knowledge","volume":"47","author":"Bateman","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis","volume":"8","author":"Haas","year":"2013","journal-title":"Nat. Protoc."},{"key":"ref_8","unstructured":"(2018, October 26). Sequence Read Archive of National Center for Biotechnology Information, Available online: https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=Cephalopoda."},{"key":"ref_9","unstructured":"(2018, October 26). Sequence Set Browser from National Center for Biotechnology Information, Available online: https:\/\/www.ncbi.nlm.nih.gov\/Traces\/wgs\/?page=1&view=TSA&search=Cephalopoda."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1007\/s00239-013-9552-5","article-title":"Molecular Phylogeny and Evolution of the Proteins Encoded by Coleoid (Cuttlefish, Octopus, and Squid) Posterior Venom Glands","volume":"76","author":"Ruder","year":"2013","journal-title":"J. Mol. Evol."},{"key":"ref_11","unstructured":"(2018, November 16). European Nucleotide Archive. Available online: https:\/\/www.ebi.ac.uk\/ena."},{"key":"ref_12","unstructured":"(2018, November 16). CLC Genomics Workbench 11.0.1. Available online: https:\/\/www.qiagenbioinformatics.com\/."},{"key":"ref_13","unstructured":"(2018, November 16). Geneious. Available online: https:\/\/www.geneious.com."},{"key":"ref_14","unstructured":"(2018, November 16). DB Browser for SQLite. Available online: https:\/\/sqlitebrowser.org\/."}],"container-title":["Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5729\/5\/4\/110\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:38:25Z","timestamp":1760179105000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5729\/5\/4\/110"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,27]]},"references-count":14,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["data5040110"],"URL":"https:\/\/doi.org\/10.3390\/data5040110","relation":{},"ISSN":["2306-5729"],"issn-type":[{"value":"2306-5729","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,27]]}}}