{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T17:05:01Z","timestamp":1769274301053,"version":"3.49.0"},"reference-count":39,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2022,2,8]],"date-time":"2022-02-08T00:00:00Z","timestamp":1644278400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"This work was supported by the International Centre for Cancer Vaccine Science, carried out within the International Research Agendas program of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fu","award":["MAB\/2017\/3"],"award-info":[{"award-number":["MAB\/2017\/3"]}]},{"name":"Dutch National Sectorplan Natuur\u2010en Scheikunde","award":["SNS\u201010.0119\/D"],"award-info":[{"award-number":["SNS\u201010.0119\/D"]}]},{"DOI":"10.13039\/501100002997","name":"Dutch Kidney Foundation","doi-asserted-by":"publisher","award":["17OKG23"],"award-info":[{"award-number":["17OKG23"]}],"id":[{"id":"10.13039\/501100002997","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>The application of proteomics to fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) human tissues is an important development spurred on by requests from stakeholder groups in clinical fields. One objective is to complement current diagnostic methods with new specific molecular information. An important goal is to achieve adequate and consistent protein recovery across and within large-scale studies. Here, we describe development of several protocols incorporating mass spectrometry compatible detergents, including Rapigest, PPS, and ProteaseMax. Methods were applied on 4 and 15 \u03bcm thick FF tissues, and 4 \u03bcm thick FFPE tissues. We evaluated sensitivity and repeatability of the methods and found that the protocol containing Rapigest enabled detection of 630 proteins from FF tissue of 1 mm2 and 15 \u03bcm thick, whereas 498 and 297 proteins were detected with the protocols containing ProteaseMax and PPS, respectively. Surprisingly, PPS-containing buffer showed good extraction of the proteins from 4 \u03bcm thick FFPE tissue with the average of 270 protein identifications (1 mm2), similar to the results on 4 \u03bcm thick FF. Moreover, we found that temperature increases during incubation with urea on 4 \u03bcm thick FF tissue revealed a decrease in the number of identified proteins and increase in the number of the carbamylated peptides.<\/jats:p>","DOI":"10.3390\/molecules27031137","type":"journal-article","created":{"date-parts":[[2022,2,8]],"date-time":"2022-02-08T23:42:20Z","timestamp":1644363740000},"page":"1137","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Evaluation of Fast and Sensitive Proteome Profiling of FF and FFPE Kidney Patient Tissues"],"prefix":"10.3390","volume":"27","author":[{"given":"Irena","family":"Dapic","sequence":"first","affiliation":[{"name":"International Centre for Cancer Vaccine Science, University of Gdansk, 80-309 Gdansk, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naomi","family":"Uwugiaren","sequence":"additional","affiliation":[{"name":"International Centre for Cancer Vaccine Science, University of Gdansk, 80-309 Gdansk, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jesper","family":"Kers","sequence":"additional","affiliation":[{"name":"Van\u2019t Hoff Institute for Molecular Sciences, University of Amsterdam, 1012 WP Amsterdam, The Netherlands"},{"name":"Department of Pathology, Amsterdam Infection & Immunity Institute (AI & II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, 1012 WP Amsterdam, The Netherlands"},{"name":"Department of Pathology, Leiden University Medical Center, 9600 Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yassene","family":"Mohammed","sequence":"additional","affiliation":[{"name":"Genome BC Proteomics Centre, University of Victoria, Victoria, BC V8Z 5N3, Canada"},{"name":"Center for Proteomics and Metabolomics, Leiden University Medical Center, 9600 Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8045-8200","authenticated-orcid":false,"given":"David R.","family":"Goodlett","sequence":"additional","affiliation":[{"name":"International Centre for Cancer Vaccine Science, University of Gdansk, 80-309 Gdansk, Poland"},{"name":"Genome BC Proteomics Centre, University of Victoria, Victoria, BC V8Z 5N3, Canada"},{"name":"Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8Z 5N3, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9423-5596","authenticated-orcid":false,"given":"Garry","family":"Corthals","sequence":"additional","affiliation":[{"name":"Van\u2019t Hoff Institute for Molecular Sciences, University of Amsterdam, 1012 WP Amsterdam, The Netherlands"},{"name":"Department of Pathology, Amsterdam University Medical Centre, University of Amsterdam, 1012 WP Amsterdam, The Netherlands"},{"name":"Maastricht MultiModal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,8]]},"reference":[{"key":"ref_1","first-page":"405","article-title":"A Proteomic Comparison of Formalin-Fixed Paraffin-Embedded Pancreatic Tissue from Autoimmune Pancreatitis, Chronic Pancreatitis, and Pancreatic Cancer","volume":"10","author":"Paulo","year":"2013","journal-title":"J. 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