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

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Item Type:Article
Title:A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis
Creators Name:Coscia, F. and Doll, S. and Bech, J.M. and Schweizer, L. and Mund, A. and Lengyel, E. and Lindebjerg, J. and Madsen, G.I. and Moreira, J.M. and Mann, M.
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 patient phenotyping using unbiased proteomics and they prove the feasibility of analyzing large tissue cohorts in a robust, timely, and streamlined manner.
Keywords:Biobank Samples, Proteomics, Mass Spectrometry, FFPE Tissue, High-Throughput, Protocol, Biomarker Discovery, Adenoma
Source:Journal of Pathology
Page Range:100-112
Date:May 2020
Official Publication:https://doi.org/10.1002/path.5420
PubMed:View item in PubMed

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