Protein Extraction of Formalin-fixed, Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass Spectrometry

• DOI: 10.1369/jhc.2009.953497
• Publication Date: 2009-05-27T02:29:13Z
• Authors: Marshall S. Scicc...; Deidre A. Dalmas; Rogely W. Boyce; Heath C. Thomas; Kendall S. Frazier
• Keywords: Mass spectrometry imaging

Global mass spectrometry (MS) profiling and spectral count quantitation are used to identify unique or differentially expressed proteins can help potential biomarkers. MS has rarely been conducted in retrospective studies, because historically, available samples for protein analyses were limited formalin-fixed, paraffin-embedded (FFPE) archived tissue specimens. Reliable methods obtaining proteomic profiles from FFPE needed. Proteomic analysis of these confounded by formalin-induced cross-linking. The performance extracted a liquid chromatography tandem format extracts whole laser capture microdissected (LCM) frozen/optimal cutting temperature (OCT)-embedded matched control rat liver compared. Extracts frozen/OCT-embedded livers atorvastatin-treated rats further compared assess the identifying atorvastatin-regulated proteins. Comparable molecular representation was found OCT-frozen sections, whereas yields slightly less sample. numbers shared identified indicated that robust LCM did not negatively affect number either samples. Subcellular similar OCT-frozen, with predominantly cytoplasmic identified. Biologically relevant changes detected samples, selected atorvastatin-related confirmed Western blot analysis. These findings demonstrate formalin fixation, paraffin processing, do impact quality quantity as determined amenable global