mTRAQ-based quantification of potential endometrial carcinoma biomarkers from archived formalin-fixed paraffin-embedded tissues

Proteomics. 2010 Sep;10(17):3108-16. doi: 10.1002/pmic.201000082.


Formalin-fixed paraffin-embedded (FFPE) tissues are the primary and preferred medium for archiving patients' samples. Here we demonstrate relative quantifications of protein biomarkers in extracts of laser microdissected epithelial cells from FFPE endometrial carcinoma tissues versus those from normal proliferative endometria by means of targeted proteomic analyses using LC-multiple reaction monitoring (MRM) MS with MRM Tags for Relative and Absolute Quantitation (mTRAQ) labeling. Comparable results of differential expressions for pyruvate kinase isoform M2 (PK-M2) and polymeric Ig receptor were observed between analyses on laser microdissected epithelial cells from FFPE tissues and corresponding homogenates from frozen tissues of the same individuals that had previously been analyzed and reported. We also identified PK-M2 in the normal proliferative phase of the endometrium. Other biomarkers in addition to PK-M2 and polymeric Ig receptor were also observed but not consistently and/or were at levels below the threshold for quantification.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Biomarkers, Tumor / analysis*
  • Biomarkers, Tumor / metabolism
  • Chromatography, Ion Exchange
  • Endometrial Neoplasms / chemistry*
  • Endometrial Neoplasms / metabolism
  • Endometrial Neoplasms / pathology
  • Epithelial Cells / metabolism
  • Female
  • Follicular Phase
  • Formaldehyde
  • Humans
  • Isotope Labeling / methods*
  • Mass Spectrometry / methods*
  • Microdissection
  • Paraffin Embedding
  • Peptide Fragments / analysis
  • Peptide Fragments / metabolism
  • Pyruvate Kinase / analysis
  • Pyruvate Kinase / metabolism
  • Receptors, Polymeric Immunoglobulin / analysis
  • Receptors, Polymeric Immunoglobulin / metabolism


  • Biomarkers, Tumor
  • Peptide Fragments
  • Receptors, Polymeric Immunoglobulin
  • Formaldehyde
  • Pyruvate Kinase