A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis

The Journal of Pathology
Fabian CosciaMatthias Mann

Abstract

Formalin fixation and paraffin-embedding (FFPE) is the most common method to preserve human tissue for clinical diagnosis, and FFPE archives represent an invaluable resource for biomedical research. Proteins in FFPE material are stable over decades but their efficient extraction and streamlined analysis by mass spectrometry (MS)-based proteomics has so far proven challenging. Herein we describe a MS-based proteomic workflow for quantitative profiling of large FFPE tissue cohorts directly from histopathology glass slides. We demonstrate broad applicability of the workflow to clinical pathology specimens and variable sample amounts, including low-input cancer tissue isolated by laser microdissection. Using state-of-the-art data dependent acquisition (DDA) and data independent acquisition (DIA) MS workflows, we consistently quantify a large part of the proteome in 100 min single-run analyses. In an adenoma cohort comprising more than 100 samples, total workup took less than a day. We observed a moderate trend towards lower protein identification in long-term stored samples (>15 years), but clustering into distinct proteomic subtypes was independent of archival time. Our results underscore the great promise of FFPE tissues for pati...Continue Reading

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Citations

Jun 25, 2020·Proteomics·Ferdinand von Eggeling, Franziska Hoffmann
Sep 23, 2020·International Journal of Molecular Sciences·Maria Hernandez-ValladaresFrode Selheim
Jan 26, 2021·Analytical Methods : Advancing Methods and Applications·Chang LiuLijiao Zhao
Dec 31, 2020·International Journal of Molecular Sciences·Aušrinė AreškevičiūtėEva L Lund
Dec 19, 2020·Molecular & Cellular Proteomics : MCP·Philipp Emanuel GeyerMatthias Mann
Jan 15, 2021·Molecular & Cellular Proteomics : MCP·Philipp E GeyerMatthias Mann
Mar 20, 2021·Current Protocols·Rachel A VictorJacob C Schwartz
Dec 31, 2020·Aging·Garik V MkrtchyanMorten Scheibye-Knudsen
May 22, 2021·Expert Review of Proteomics·Morgan Mann, Allan R Brasier
May 28, 2021·The Analyst·Yiheng MaoRuijun Tian
Jun 29, 2021·Advanced Drug Delivery Reviews·Qi XiaoTiannan Guo
Mar 24, 2021·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Cyril DourtheAnne-Aurélie Raymond
Sep 2, 2021·Expert Review of Proteomics·Jacqueline S Gerritsen, Forest M White
Aug 31, 2021·Clinical and Translational Medicine·Erika VelasquezGyörgy Marko-Varga
Nov 5, 2021·Journal of Proteome Research·Stephan EckertBernhard Kuster

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