NIH, National Cancer Institute, Division of Cancer Treatment and Diagnosis (DCTD) NIH - National Institutes of Health National Cancer Institute DCTD - Division of Cancer Treatment and Diagnosis

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

Author(s): DeSouza LV, Krakovska O, Darfler MM, Krizman DB, Romaschin AD, Colgan TJ, Siu KW

Publication: Proteomics, 2010, Vol. 10, Page 3108-16

PubMed ID: 20661955 PubMed Review Paper? No

Purpose of Paper

The purpose of this paper was to determine if relative protein levels were comparable between formalin-fixed paraffin-embedded (FFPE) and frozen specimens by multiple reaction monitoring (MRM) mass spectrometry (MS) methods.

Conclusion of Paper

The relative amount of pyruvate kinase (PK) and polymeric immunoglobulin receptor (PIGR) were consistent between 3 of 4 sets of frozen and FFPE specimens. The authors state that the peak ratios obtained using MRM Tags for Relative and Absolute Quantitation (mTRAQ) were more consistent with dot blot intensities than peak ratios obtained using isobaric tags for relative and absolute quantitation (iTRAQ).


  1. Study Purpose

    The purpose of this study was to determine the effects of using FFPE rather than frozen specimens and MRM MS method on relative quantification of proteins. 3 endometrial carcinoma specimens and 1 normal proliferative were fixed for at least 2 days before paraffin-embedding with some specimens fixed for as long as 6 days. Protein was extracted from 6-8 laser microdissected sections.

    Summary of Findings:

    The relative amount of PK was consistent between frozen and FFPE specimens for at least 3 of 4 specimens. Further, the intensities of PIGR in the spectra from FFPE specimens corresponded with the relative intensities by Western blot for 3 of 4 frozen specimens. The author attribute differences between frozen and FFPE specimens to specimen heterogeneity. The authors state that the peak ratios obtained from FFPE specimens by mTRAQ labeling better correlate with dot blot data from frozen specimens than the peak ratios obtained from frozen specimens using iTRAQ labeling.

    Preservative Types
    • Frozen
    • Formalin
    • Neoplastic - Carcinoma
    • Normal
    AnalyteTechnology Platform
    Protein Western blot
    Peptide LC-MS or LC-MS/MS
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
    LC-MS or LC-MS/MS Specific Targeted peptide/protein PIGR
    LC-MS or LC-MS/MS Specific Detection method mTRAQ

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