{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T21:34:36Z","timestamp":1774820076124,"version":"3.50.1"},"reference-count":54,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2021,11,16]],"date-time":"2021-11-16T00:00:00Z","timestamp":1637020800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Interreg POCTEP","award":["07-12-ACUINANO_1_E"],"award-info":[{"award-number":["07-12-ACUINANO_1_E"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["UIDB\/04423\/2020"],"award-info":[{"award-number":["UIDB\/04423\/2020"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["UIDP\/04423\/2020"],"award-info":[{"award-number":["UIDP\/04423\/2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteomes"],"abstract":"<jats:p>Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC\u2013MS\/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).<\/jats:p>","DOI":"10.3390\/proteomes9040046","type":"journal-article","created":{"date-parts":[[2021,11,17]],"date-time":"2021-11-17T21:32:07Z","timestamp":1637184727000},"page":"46","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2552-6853","authenticated-orcid":false,"given":"M\u00e1rio Jorge","family":"Ara\u00fajo","sequence":"first","affiliation":[{"name":"CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"}]},{"given":"Maria L\u00edgia","family":"Sousa","sequence":"additional","affiliation":[{"name":"CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"}]},{"given":"Aldo Barreiro","family":"Felpeto","sequence":"additional","affiliation":[{"name":"CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"}]},{"given":"Maria V.","family":"Turkina","sequence":"additional","affiliation":[{"name":"Department of Biomedical and Clinical Sciences, Faculty of Medicine and Clinical Sciences, Link\u00f6ping University, 581 83 Link\u00f6ping, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8955-2108","authenticated-orcid":false,"given":"Elza","family":"Fonseca","sequence":"additional","affiliation":[{"name":"CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2134-6169","authenticated-orcid":false,"given":"Jos\u00e9 Carlos","family":"Martins","sequence":"additional","affiliation":[{"name":"CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3585-2417","authenticated-orcid":false,"given":"V\u00edtor","family":"Vasconcelos","sequence":"additional","affiliation":[{"name":"CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"},{"name":"Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s\/n, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4621-885X","authenticated-orcid":false,"given":"Alexandre","family":"Campos","sequence":"additional","affiliation":[{"name":"CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Nilo-Poyanco, R., Moraga, C., Benedetto, G., Orellana, A., and Almeida, A.M. (2021). Shotgun Proteomics of Peach Fruit Reveals Major Metabolic Pathways Associated to Ripening. BMC Genom., 22.","DOI":"10.1186\/s12864-020-07299-y"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1016\/j.jprot.2010.08.005","article-title":"Advances in shotgun proteomics and the analysis of membrane proteomes","volume":"73","author":"Gilmore","year":"2010","journal-title":"J. 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