{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T22:41:07Z","timestamp":1762641667189,"version":"3.38.0"},"reference-count":35,"publisher":"SAGE Publications","issue":"3","license":[{"start":{"date-parts":[[2014,6,1]],"date-time":"2014-06-01T00:00:00Z","timestamp":1401580800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Eur J Mass Spectrom (Chichester)"],"published-print":{"date-parts":[[2014,6]]},"abstract":"<jats:p> In bottom-up proteomics approaches, the enzymatic proteolysis step before mass spectrometry (MS) analysis is of crucial importance, as only the efficient digestion of the protein will ensure its accurate quantification. The structural and chemical alterations occurring upon protein oxidation may decrease the efficiency of trypsin digestion, compromising the ensuing MS analysis. Herein, the efficiency of the trypsin digestion of oxidized bovine serum albumin (BSA) was assessed by protein-sequence coverage and the exponentially modified protein abundance index (emPAI) algorithm, allowing a comparison of protein abundance in samples with different levels of oxidation. Despite the extensive oxidation induced to BSA, verified by analysis of protein carbonyls, no significant difference in the yield of tryptic peptides from oxidized samples could be observed by nano-high-performance liquid chromatography (HPLC) and nano-HPLC\u2013electrospray ionization\u2013MS analysis. After a database search, similar protein-sequence coverage rates were obtained for both treated and control samples. Thus, exponentially modified protein abundance index scores confirmed that, regardless of being oxidized, the same amount of BSA was present in the sodium dodecyl sulfate\/polyacrylamide gel electrophoresis bands excised for digestion. The obtained results show that the digestion of the control and oxidized samples were similar, leading to the conclusion that in-gel proteolysis is not a main hindrance for the identification and quantification of oxidized proteins by MS. <\/jats:p>","DOI":"10.1255\/ejms.1279","type":"journal-article","created":{"date-parts":[[2014,8,22]],"date-time":"2014-08-22T17:20:28Z","timestamp":1408728028000},"page":"271-278","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":3,"title":["Efficiency of Trypsin Digestion for Mass-Spectrometry-Based Identification and Quantification of Oxidized Proteins: Evaluation of the Digestion of Oxidized Bovine Serum Albumin"],"prefix":"10.1177","volume":"20","author":[{"given":"Duarte D.","family":"Gouveia","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"given":"Andr\u00e9 M.N.","family":"Silva","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal"},{"name":"REQUIMTE\/Departmento de Qu\u00edmica e Bioquimica, Faculdade de Ci\u00eancias da Universidade do Porto, Rua do Campo Alegre S\/N, 4169-007 Porto, Portugal"}]},{"given":"Rui","family":"Vitorino","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"given":"M. Ros\u00e1rio M.","family":"Domingues","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"given":"Pedro","family":"Domingues","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal"}]}],"member":"179","published-online":{"date-parts":[[2014,6,1]]},"reference":[{"key":"bibr1-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1002\/mas.20006"},{"key":"bibr2-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.272.33.20313"},{"key":"bibr3-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbapap.2004.08.007"},{"key":"bibr4-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/j.freeradbiomed.2006.08.013"},{"key":"bibr5-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/j.freeradbiomed.2013.08.184"},{"key":"bibr6-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1007\/s00726-010-0585-4"},{"key":"bibr7-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1039\/c0ay00375a"},{"key":"bibr8-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2004.08.013"},{"key":"bibr9-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200401268"},{"key":"bibr10-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/j.jasms.2004.02.005"},{"key":"bibr11-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/j.ab.2009.05.050"},{"key":"bibr12-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1021\/cr068213f"},{"key":"bibr13-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-005-5160-x"},{"key":"bibr14-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-30379-6_14"},{"key":"bibr15-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1021\/pr060021d"},{"key":"bibr16-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200900502"},{"key":"bibr17-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/j.jprot.2011.05.004"},{"key":"bibr18-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M500061-MCP200"},{"key":"bibr19-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.4149"},{"key":"bibr20-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(94)33040-9"},{"key":"bibr21-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-8981(03)00003-2"},{"key":"bibr22-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-60327-259-9_27"},{"key":"bibr23-ejms.1279","volume":"5423","author":"Zhu K.","year":"2006","journal-title":"Bio-Rad Bulletin"},{"key":"bibr24-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1042\/bj2500087"},{"key":"bibr25-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-4838(96)00180-X"},{"key":"bibr26-ejms.1279","doi-asserted-by":"publisher","DOI":"10.1021\/ac0484373"},{"key":"bibr27-ejms.1279","first-page":"73","volume-title":"Integrative Proteomics","author":"Hustoft H.M. 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