Open AccessProteome Analysis of Microdissected Formalin-fixed and Paraffin-embedded Tissue Specimens
Author(s) -
Tong Guo,
Weijie Wang,
Paul Rudnick,
Tao Song,
Jie Li,
Zhengping Zhuang,
Robert J. Weil,
Don L. DeVoe,
Cheng S. Lee,
Brian M. Balgley
Publication year - 2007
Publication title -
journal of histochemistry and cytochemistry/the journal of histochemistry and cytochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.971
H-Index - 124
eISSN - 1551-5044
pISSN - 0022-1554
DOI - 10.1369/jhc.7a7177.2007
Subject(s) - proteome , proteomics , isoelectric focusing , tandem mass spectrometry , biomarker discovery , biomarker , biology , pathology , chemistry , mass spectrometry , chromatography , medicine , bioinformatics , biochemistry , enzyme , gene
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.