Proteomic Analysis of Formalin-fixed Prostate Cancer Tissue

Author(s): Hood BL, Darfler MM, Guiel TG, Furusato B, Lucas DA, Ringeisen BR, Sesterhenn IA, Conrads TP, Veenstra TD, Krizman DB

Publication: Mol Cell Proteomics, 2005, Vol. 4, Page 1741

PubMed ID: 16091476 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   To assess the applicability of microdissected cells from FFPE tissue sections for detection and quantitative analysis using microarray analysis following the biochemical recovery of soluble proteins and peptides.

   Summary of Findings:

   PSA was appropriately and dose-dependently detected in serially diluted protein extracts isolated from microdissected prostate regions, indicating successful application of FFPE microdissected cells and the protein microarray platform.

   Biospecimens

   • Tissue - Prostate

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Carcinoma
   • Neoplastic - Benign

   Platform:

   Analyte	Technology Platform
   Protein	Reverse phase protein microarray

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Aliquots and Components	Aliquot size/volume	0.05 Dilution factor 0.125 Dilution factor 0.25 Dilution factor 0.50 Dilution factor

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2. Study Purpose

   To determine the feasibility of peptide identification via conventional mass spectrometry in cells microdissected from FFPE tissue.

   Summary of Findings:

   Nano RPLC-mass spectrometry analysis of extracts from PSA-positive and -negative FFPE microdissected regions yielded thousands of unique tryptic peptides representing hundreds of unique proteins. Identified proteins encompassed a range of functions and included cytoskeletal, prostate-related, and signal transduction proteins. A portion of the identified peptides contained formylated lysl residues (6.5%), and oxidized methionine residues (53%). Although the number of peptides with arginyl and lysl termini were slightly elevated, they did not differ significantly from theorteical occurrence. The number of identified proteins containing an internal missed cleavage site was at the high end of the predicted spectrum (25%). Quantitative protein profiling yielded differential protein expression between the two microdissected regions (PCA-positive vs -negative).

   Biospecimens

   • Tissue - Prostate

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Benign
   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   Peptide	GC-MS

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Analyte Extraction and Purification	Analyte isolation method	Tissue microdissection

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