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Impact of fixation time on GeLC–MS/MS proteomic profiling of formalin-fixed, paraffin-embedded tissues

Tanca, Alessandro and Pagnozzi, Daniela and Falchi, Giovanni and Biosa, Grazia and Rocca, Stefano and Foddai, Gisella and Uzzau, Sergio and Addis, Maria Filippa (2011) Impact of fixation time on GeLC–MS/MS proteomic profiling of formalin-fixed, paraffin-embedded tissues. Journal of Proteomics, Vol. 74 (7), p. 1015-1021. ISSN 1874-3919. eISSN 1876-7737. Article.

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DOI: 10.1016/j.jprot.2011.03.015

Abstract

Formalin-fixed, paraffin-embedded (FFPE) tissue banks represent an invaluable resource for biomarker discovery. Recently, the combination of full-length protein extraction, GeLC–MS/MS analysis, and spectral counting quantification has been successfully applied to mine proteomic information from these tissues. However, several sources of variability affect these samples; among these, the duration of the fixation process is one of the most important and most easily controllable ones. To assess its influence on quality of GeLC–MS/MS data, the impact of fixation time on efficiency of full-length protein extraction efficiency and on quality of label-free quantitative data was evaluated.
As a result, although proteins were successfully extracted from FFPE liver samples fixed for up to eight days, fixation time appeared to negatively influence both protein extraction yield and GeLC–MS/MS quantitative proteomic data. Particularly, MS identification efficiency decreased with increasing fixation times. Moreover, amino acid modifications putatively induced by formaldehyde were detected and characterized.
These results demonstrate that proteomic information can be achieved also from tissue samples fixed for relatively long times, but suggest that variations in fixation time need to be carefully taken into account when performing proteomic biomarker discovery studies on fixed tissue archives.

Item Type:Article
ID Code:6223
Status:Published
Refereed:Yes
Uncontrolled Keywords:FFPE, GeLC–MS/MS, fixation time, formaldehyde, proteomics
Subjects:Area 06 - Scienze mediche > MED/07 Microbiologia e microbiologia clinica
Area 07 - Scienze agrarie e veterinarie > VET/03 Patologia generale e anatomia patologica veterinaria
Divisions:001 Università di Sassari > 01 Dipartimenti > Patologia e clinica veterinaria
001 Università di Sassari > 01 Dipartimenti > Scienze biomediche
002 Altri enti e centri di ricerca del Nord Sardegna > Porto Conte Ricerche, Alghero
Publisher:Elsevier
ISSN:1874-3919
eISSN:1876-7737
Copyright Holders:© 2011 Elsevier B.V.
Additional Information:Title of issue: Mass Spectrometry - One of the pillars of proteomics, edited by Martina Marchetti, Deschmann and Gunter Allmaier
Deposited On:06 Jul 2011 13:52

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