Proteomic developments in the analysis of formalin-fixed tissue

Abstract

Retrospective proteomic studies, including those which aim to elucidate the molecular mechanisms driving cancer, require the assembly and characterization of substantial patient tissue cohorts. The difficulty of maintaining and accessing native tissue archives has prompted the development of methods to access archives of formalin-fixed tissue. Formalin-fixed tissue archives, complete with patient meta data, have accumulated for decades, presenting an invaluable resource for these retrospective studies. This review presents the current knowledge concerning formalin-fixed tissue, with descriptions of the mechanisms of formalin fixation, protein extraction, top-down proteomics, bottom-up proteomics, quantitative proteomics, phospho- and glycoproteomics as well as imaging mass spectrometry. Particular attention has been given to the inclusion of proteomic investigations of archived tumour tissue. This article is part of a Special Issue entitled: Medical Proteomics.

Proteomics of ovarian cancer: functional insights and clinical applications

“…Unfortunately, formalin in these specimens was found to form crosslinks that mask epitopes and reduce the yield of protein from tissue. However, in recent years, analysis of FFPE specimens has improved enormously due to advances in protein extraction protocols ( reviewed here [23]). Laser capture microdissection is a novel technique that has been employed to reduce within tumor heterogeneity.…”

Proteomic analysis of FFPE tissue: barriers to clinical impact

“…This editorial focuses on the barriers that must be overcome for FFPE tissues to impact clinical molecular diagnosis. An overview of FFPE tissue proteomics is provided in the excellent review of Gustafsson et al [2].…”

“…Over the past few years, advances in methodology have made it possible to recover proteins or peptides from FFPE tissue, yielding a reasonable representation of the proteins recovered from matched fresh or frozen specimens. Early qualitative approaches have given way to quantitative proteomic analysis of FFPE tissues [2]. An encouraging recent trend is the validation of quantitative FFPE proteomics findings using orthogonal methods such as immunohistochemistry and immunoblotting [3,4].…”

Insights into autosomal dominant polycystic kidney disease by quantitative mass spectrometry-based proteomics

“…To improve our understanding of proteome alterations under pathological conditions, methods have been developed to analyze formalin-fixed paraffin-embedded (FFPE) tissues specimens by MS analyses (Ostasiewicz et al 2010; for detailed technical information, see also Gustafsson et al 2015;Maes et al 2013). FFPE tissue specimens represent preserved clinical material that is a unique protein source for studying human disorders and for the identification of disease biomarkers.…”