{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T20:00:08Z","timestamp":1773864008540,"version":"3.50.1"},"reference-count":14,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2019,4,10]],"date-time":"2019-04-10T00:00:00Z","timestamp":1554854400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J Mass Spectrom"],"published-print":{"date-parts":[[2020,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Formalin\u2010fixed and paraffin\u2010embedded (FFPE)\u2013tissue archives are potential treasure troves in the search for clinically interesting specimens. However, while the FFPE\u2010treatment provides excellent conservation of the three\u2010dimensional structure of the tissue and prevents degradation over decades, it also introduces numerous nonspecific and irreversible protein modifications. In this study, we have evaluated several published workflows for FFPE\u2010tissue by fit\u2010for\u2010purpose proteomics technologies. We demonstrate that many protein modifications and cross\u2010links remain after treatment and conclude that the proteomics of FFPE\u2010tissue is of value, but clear\u2010cut limitations must be kept in mind. The analysis of abundant proteins in FFPE is straightforward, but confident identification of low\u2010level proteins and\/or biologically relevant modifications is seriously hampered by the FFPE\u2010treatment. Peptide assignment should only be performed on high\u2010quality spectra, even if this is at the cost of lower numbers of protein IDs. As Yergey and Coorssen stated in 2015: \u201cData quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis.\u201d<\/jats:p>","DOI":"10.1002\/jms.4347","type":"journal-article","created":{"date-parts":[[2019,3,3]],"date-time":"2019-03-03T20:35:21Z","timestamp":1551645321000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Are formalin\u2010fixed and paraffin\u2010embedded tissues fit for proteomic analysis?"],"prefix":"10.1002","volume":"55","author":[{"given":"Malte","family":"Bayer","sequence":"first","affiliation":[{"name":"Core Unit Proteomics, Interdisciplinary Center for Clinical Research, Medical Faculty University of M\u00fcnster  M\u00fcnster Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linus","family":"Angenendt","sequence":"additional","affiliation":[{"name":"Department of Medicine A, Haematology and Oncology University Hospital M\u00fcnster  M\u00fcnster Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christoph","family":"Schliemann","sequence":"additional","affiliation":[{"name":"Department of Medicine A, Haematology and Oncology University Hospital M\u00fcnster  M\u00fcnster Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolfgang","family":"Hartmann","sequence":"additional","affiliation":[{"name":"Gerhard\u2010Domagk\u2010Institute of Pathology University Hospital M\u00fcnster  M\u00fcnster Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0672-7246","authenticated-orcid":false,"given":"Simone","family":"K\u00f6nig","sequence":"additional","affiliation":[{"name":"Core Unit Proteomics, Interdisciplinary Center for Clinical Research, Medical Faculty University of M\u00fcnster  M\u00fcnster Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2019,4,10]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jpba.2018.03.065"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.2144\/000114414"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/prca.201200046"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/ardp.19122500151"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1021\/bc050340f"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0142650"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/labinvest.2016.134"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1039\/C5MB00670H"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr100234w"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/0307-4412(83)90048-1"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200800971"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2016.042"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jprot.2018.05.016"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaut.2019.03.004"}],"container-title":["Journal of Mass Spectrometry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjms.4347","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jms.4347","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T18:05:50Z","timestamp":1760637950000},"score":1,"resource":{"primary":{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/10.1002\/jms.4347"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4,10]]},"references-count":14,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2020,8]]}},"alternative-id":["10.1002\/jms.4347"],"URL":"https:\/\/doi.org\/10.1002\/jms.4347","archive":["Portico"],"relation":{},"ISSN":["1076-5174","1096-9888"],"issn-type":[{"value":"1076-5174","type":"print"},{"value":"1096-9888","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,10]]},"assertion":[{"value":"2018-11-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-02-25","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-04-10","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e4347"}}