title: Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives.
abstract: Formalin-fixed paraffin-embedded (FFPE) tissues are a real treasure for retrospective analysis considering the amount of samples present in hospital archives, combined with pathological, clinical, and outcome information available for every sample. Although unlocking the proteome of these tissues is still a challenge, new approaches are being developed. In this review, we summarize the different mass spectrometry platforms that are used in human clinical studies to unravel the FFPE proteome. The different ways of extracting crosslinked proteins and the analytical strategies are pointed out. Also, the pitfalls and challenges concerning the quality of FFPE proteomic approaches are depicted. We also evaluated the potential of these analytical methods for future clinical FFPE proteomics applications.
authors.affiliation: Research Group of Functional Genomics and Proteomics, University of Leuven, Belgium. evelyne.maes@bio.kuleuven.be
authors.forename: Evelyne
authors.initials: E
authors.lastname: Maes
authors.forename: Valérie
authors.initials: V
authors.lastname: Broeckx
authors.forename: Inge
authors.initials: I
authors.lastname: Mertens
authors.forename: Xavier
authors.initials: X
authors.lastname: Sagaert
authors.forename: Hans
authors.initials: H
authors.lastname: Prenen
authors.forename: Bart
authors.initials: B
authors.lastname: Landuyt
authors.forename: Liliane
authors.initials: L
authors.lastname: Schoofs
mesh_terms: D002853:Chromatography, Liquid; D005404:Fixatives; D005557:Formaldehyde; D006801:Humans; D013058:Mass Spectrometry; D016612:Paraffin Embedding; D011506:Proteins / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D012189:Retrospective Studies; D016707:Tissue Fixation; D014021:Tissue Preservation / Q000379:methods*
chemical_list: D005404:Fixatives; D011506:Proteins; D020543:Proteome; D005557:Formaldehyde