Qualitative and quantitative proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue

Omid Azimzadeh; Michael J. Atkinson; Soile Tapio

doi:10.1007/978-1-4939-2550-6_10

Qualitative and quantitative proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue

Omid Azimzadeh
, Michael J. Atkinson
, Soile Tapio

Technical University of Munich

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Abstract

Formalin-fixed, paraffin-embedded (FFPE) tissue has recently gained interest as an alternative to fresh/ frozen tissue for retrospective protein biomarker discovery. However, during the formalin fixation proteins undergo degradation and cross-linking, making conventional protein analysis technologies challenging. Cross-linking is even more challenging when quantitative proteome analysis of FFPE tissue is planned. The use of conventional protein labeling technologies on FFPE tissue has turned out to be problematic as the lysine residue labeling targets are frequently blocked by the formalin treatment. We have established a qualitative and quantitative proteomics analysis technique for FFPE tissues that combines label-free proteomic analysis with optimized protein extraction and separation conditions.

Original language	English
Pages (from-to)	109-115
Number of pages	7
Journal	Methods in molecular biology (Clifton, N.J.)
Volume	1295
DOIs	https://doi.org/10.1007/978-1-4939-2550-6_10
State	Published - 4 Dec 2014

Keywords

Biomarker discovery
Formalin-fixed paraffin embedded (FFPE)
Label-free proteomics
Mass spectrometry
Peptide modification

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10.1007/978-1-4939-2550-6_10

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abstract = "Formalin-fixed, paraffin-embedded (FFPE) tissue has recently gained interest as an alternative to fresh/ frozen tissue for retrospective protein biomarker discovery. However, during the formalin fixation proteins undergo degradation and cross-linking, making conventional protein analysis technologies challenging. Cross-linking is even more challenging when quantitative proteome analysis of FFPE tissue is planned. The use of conventional protein labeling technologies on FFPE tissue has turned out to be problematic as the lysine residue labeling targets are frequently blocked by the formalin treatment. We have established a qualitative and quantitative proteomics analysis technique for FFPE tissues that combines label-free proteomic analysis with optimized protein extraction and separation conditions.",

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AU - Atkinson, Michael J.

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KW - Mass spectrometry

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Qualitative and quantitative proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue

Abstract

Keywords

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