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Originally published as JHC exPRESS on April 4, 2007.
doi:10.1369/jhc.7A7177.2007
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Journal of Histochemistry and Cytochemistry
Volume 55 (7): 763-772, 2007
Copyright ©The Histochemical Society, Inc.

Proteome Analysis of Microdissected Formalin-fixed and Paraffin-embedded Tissue Specimens

Tong Guo, Weijie Wang, Paul A. Rudnick, Tao Song, Jie Li, Zhengping Zhuang, Robert J. Weil, Don L. DeVoe, Cheng S. Lee and Brian M. Balgley

Department of Chemistry and Biochemistry (TG,CSL) and Department of Mechanical Engineering and Bioengineering Program (DLD), University of Maryland, College Park, Maryland; Calibrant Biosystems, Gaithersburg, Maryland (WW,PAR,TS,BMB); Molecular Pathogenesis Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland (JL,ZZ); and Brain Tumor Institute, Cleveland Clinic Foundation, Cleveland, Ohio (RJW)

Correspondence to: Brian M. Balgley, Calibrant Biosystems, 910 Clopper Road, Suite 220N, Gaithersburg, MD 20878. E-mail: brian.balgley{at}calibrant.com

Targeted proteomics research, based on the enrichment of disease-relevant proteins from isolated cell populations selected from high-quality tissue specimens, offers great potential for the identification of diagnostic, prognostic, and predictive biological markers for use in the clinical setting and during preclinical testing and clinical trials, as well as for the discovery and validation of new protein drug targets. Formalin-fixed and paraffin-embedded (FFPE) tissue collections, with attached clinical and outcome information, are invaluable resources for conducting retrospective protein biomarker investigations and performing translational studies of cancer and other diseases. Combined capillary isoelectric focusing/nano-reversed-phase liquid chromatography separations equipped with nano-electrospray ionization-tandem mass spectrometry are employed for the studies of proteins extracted from microdissected FFPE glioblastoma tissues using a heat-induced antigen retrieval (AR) technique. A total of 14,478 distinct peptides are identified, leading to the identification of 2733 non-redundant SwissProt protein entries. Eighty-three percent of identified FFPE tissue proteins overlap with those obtained from the pellet fraction of fresh-frozen tissue of the same patient. This large degree of protein overlapping is attributed to the application of detergent-based protein extraction in both the cell pellet preparation protocol and the AR technique. (J Histochem Cytochem 55:763–772, 2007)

Key Words: proteomics • mass spectrometry • formalin-fixed • tissue • microdissection


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