{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T08:45:27Z","timestamp":1790153127831,"version":"4.0.1"},"reference-count":26,"publisher":"Wiley","issue":"21","license":[{"start":{"date-parts":[[2022,9,20]],"date-time":"2022-09-20T00:00:00Z","timestamp":1663632000000},"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":["Proteomics"],"published-print":{"date-parts":[[2022,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Tissue biopsies are most commonly archived in a paraffin block following tissue fixation with formaldehyde (FFPE) or as fresh frozen tissue (FFT). While both methods preserve biological samples, little is known about how they affect the quantifiable proteome. We performed a \u2018bottom\u2010up\u2019 proteomic analysis (\n                    <jats:italic>N<\/jats:italic>\n                    \u00a0=\u00a020) of short and long\u2010term archived FFPE surgical samples of human meningiomas and compared them to matched FFT specimens. FFT facilitated a similar number of proteins assigned by MetaMorpheus compared with matched FFPE specimens (5378\u00a0vs. 5338 proteins, respectively (\n                    <jats:italic>p<\/jats:italic>\n                    \u00a0=\u00a00.053), regardless of archival time. However, marked differences in the proteome composition were apparent between FFPE and FFT specimens. Twenty\u2010three percent of FFPE\u2010derived peptides and 8% of FFT\u2010derived peptides contained at least one chemical modification. Methylation and formylation were most prominent in FFPE\u2010derived peptides (36% and 17% of modified FFPE peptides, respectively) while, most of phosphorylation and iron modifications appeared in FFT\u2010derived peptides (\n                    <jats:italic>p<\/jats:italic>\n                    \u00a0&lt;\u00a00.001). A mean 14% (\u00b1\u00a02.9) of peptides identified in FFPE contained at least one modified Lysine residue. Importantly, larger proteins were significantly overrepresented in FFT specimens, while FFPE specimens were enriched with smaller proteins.\n                  <\/jats:p>","DOI":"10.1002\/pmic.202200085","type":"journal-article","created":{"date-parts":[[2022,9,13]],"date-time":"2022-09-13T05:35:13Z","timestamp":1663047313000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Comparison of matched formalin\u2010fixed paraffin embedded and fresh frozen meningioma tissue reveals bias in proteomic profiles"],"prefix":"10.1002","volume":"22","author":[{"given":"Hanan","family":"Schoffman","sequence":"first","affiliation":[{"name":"Laboratory of Molecular Neuro Oncology, Neurosurgery Department Shaare Zedek Medical Center  Jerusalem Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yishai","family":"Levin","sequence":"additional","affiliation":[{"name":"de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine Weizmann Institute of Science  Rehovot Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayelet","family":"Itzhaki\u2010Alfia","sequence":"additional","affiliation":[{"name":"Department of Pathology Tel Aviv Sourasky Medical Center  Tel Aviv Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lea","family":"Tselekovits","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Neuro Oncology, Neurosurgery Department Shaare Zedek Medical Center  Jerusalem Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lior","family":"Gonen","sequence":"additional","affiliation":[{"name":"Neurosurgery Department, Shaare Zedek Medical Center Hebrew University Medical School  Jerusalem Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8828-8138","authenticated-orcid":false,"given":"Gilad Wolf","family":"Vainer","sequence":"additional","affiliation":[{"name":"Department of Pathology Hadassah Hebrew University Medical School  Jerusalem Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Goni","family":"Hout\u2010Siloni","sequence":"additional","affiliation":[{"name":"Department of Pathology Sheba Medical Center  Ramat Gan Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iris","family":"Barshack","sequence":"additional","affiliation":[{"name":"Department of Pathology Sheba Medical Center  Ramat Gan Israel"},{"name":"Sackler Faculty of Medicine Tel Aviv University  Tel Aviv Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zvi R.","family":"Cohen","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery Sheba Medical Center  Ramat Gan Israel"},{"name":"Sackler Faculty of Medicine Tel Aviv University  Tel Aviv Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nevo","family":"Margalit","sequence":"additional","affiliation":[{"name":"Neurosurgery Department, Shaare Zedek Medical Center Hebrew University Medical School  Jerusalem Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0293-0431","authenticated-orcid":false,"given":"Tal","family":"Shahar","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Neuro Oncology, Neurosurgery Department Shaare Zedek Medical Center  Jerusalem Israel"},{"name":"Neurosurgery Department, Shaare Zedek Medical Center Hebrew University Medical School  Jerusalem Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,9,20]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M500102\u2010MCP200"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/labinvest.3700343"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr050208p"},{"issue":"8","key":"e_1_2_10_5_1","first-page":"1160","article-title":"Proteomics for cancer biomarker discovery","volume":"48","author":"Srinivas P. 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