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. Author manuscript; available in PMC: 2016 Sep 9.
Published in final edited form as: J Proteome Res. 2016 Jul 27;15(8):2717–2728. doi: 10.1021/acs.jproteome.6b00245

Figure 4. Comparison of protein quantification in matched frozen and FFPE biospecimens.

Figure 4

Three individual breast cancer tissues were sectioned and analyzed by multiplexed LC-MRM (targeting 512 peptide analytes) and immuno-MRM (targeting 42 peptide analytes) assays. Each sample was analyzed in process triplicate, and each replicate consisted of extraction, digestion, and enrichment performed on three separate days. A. Protein recovery from matched FFPE and frozen samples measured by BCA assay. B. Overlap in number of peptides detected in quantitative LC-MRM and immuno-MRM assays in matched FFPE and frozen tissue specimens. C. Scatter plot of endogenous peptide concentrations (n= 356) determined by MRM measurements made in the matched FFPE and frozen tissue. D. Repeatability (CV) of immuno-MRM and LC-MRM assays applied to FFPE and frozen tissue, each box plot represents three samples measured on three days (n = 9). E. Scatter plot of endogenous peptides (n= 49) with overlapping immuno-MRM and LC-MRM measurements in FFPE (yellow) and frozen (blue) tissues. Error bars are the standard deviation of triplicate measurements.