A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis
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A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis. / Coscia, Fabian; Doll, Sophia; Bech, Jacob Mathias; Schweizer, Lisa; Mund, Andreas; Lengyel, Ernst; Lindebjerg, Jan; Madsen, Gunvor Iben; Moreira, José M A; Mann, Matthias.
In: Journal of Pathology, Vol. 251, 2020, p. 110-112.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis
AU - Coscia, Fabian
AU - Doll, Sophia
AU - Bech, Jacob Mathias
AU - Schweizer, Lisa
AU - Mund, Andreas
AU - Lengyel, Ernst
AU - Lindebjerg, Jan
AU - Madsen, Gunvor Iben
AU - Moreira, José M A
AU - Mann, Matthias
PY - 2020
Y1 - 2020
N2 - 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. Here, we describe an 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 (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 work up took less than a day. We observed a moderate trend towards lower protein identifications in long-term stored samples (>15 years) but clustering into distinct proteomic subtypes was independent of archival time. Our results underline the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and prove the feasibility of analyzing large tissue cohorts in a robust, timely and streamlined manner. This article is protected by copyright. All rights reserved.
AB - 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. Here, we describe an 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 (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 work up took less than a day. We observed a moderate trend towards lower protein identifications in long-term stored samples (>15 years) but clustering into distinct proteomic subtypes was independent of archival time. Our results underline the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and prove the feasibility of analyzing large tissue cohorts in a robust, timely and streamlined manner. This article is protected by copyright. All rights reserved.
U2 - 10.1002/path.5420
DO - 10.1002/path.5420
M3 - Journal article
C2 - 32154592
VL - 251
SP - 110
EP - 112
JO - Journal of Pathology
JF - Journal of Pathology
SN - 0022-3417
ER -
ID: 239206071