Quantify Multiplex Biomarkers in Formalin Fixed Paraffin Embedded Tissue Using MRM

Power of quantitative proteomics applied to FFPE tumor specimens

Protein biomarkers can provide critical insights into patient responses and measuring them in FFPE (formalin-fixed paraffin embedded) tissue samples has become standard practice.

These samples are usually stored at ambient temperature, stable for a long period of time, and easily accessible through tissue banks for retrospective discovery and targeted analysis.

One of the challenges faced in clinical research as well as in clinical trials is availability of sample amounts for the development and testing of quantitative biomarkers.

Mass spectrometry (MS)-based quantitative proteomics overcomes this hurdle by allowing measurement of biomarkers in large sample sets using small amounts of FFPE samples.

CellCarta can rapidly develop assays to quantify proteins of interest in FFPE tissue samples. Our protocols, compliant with GCLP standards, are robust, reproducible, and accurate.

Quantify Multiplex Biomarkers in Formalin-Fixed Paraffin Embedded Tissue Samples using MRM

Our Multiple Reaction Monitoring (MRM) assays quantify protein biomarkers of interest in FFPE samples with a degree of precision and accuracy comparable to immunoassays but without the need for antibodies.

Given its specificity, its selectivity, and its ability to deliver accurate measurements, mass spectrometry is complementary to the immunohistochemistry (IHC) approach.

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Our platform provides the following features:

  • Specificity provided by the targeted approach and use of heavy-labeled standards
  • Sensitivity for detection of endogenous levels in small tissue material as low as 5μg
  • Reproducibility and accuracy across the detection range maintained throughout the study
  • Multiplex capabilities that allow simultaneous quantification of different proteins
  • Option to perform assay under GCLP and CAP/CLIA environments for clinical trial samples
  • Pathologist-guided specimen dissection for accurate selection of tumor tissue section
  • Rapid assay development, with timelines relevant to clinical trials
  • Assay validation following the CPTAC guidelines


A targeted proteomics approach for analyzing FFPE tissue in clinical research

At CellCarta, we have established an efficient analytical workflow within CAP-accredited, CLIA-certified, and GCLP regulatory environments.

From protein extraction to quantification by MRM, all assay parameters were comprehensively characterized.

For MRM, these included specificity, interference, carryover, precision & accuracy, and matrix effects.

A concrete example of this approach is our fit-for-purpose assay developed to quantify 12 biomarkers, including HER2, in clinical samples.

This multiplexed assay was validated using FFPE tissues samples from colorectal cancer patients.

For more information on our off-the-shelf MS assays

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