Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new tissue biomarkers have been translated into clinical use. Clinical validation studies must be performed on large numbers of candidates for a single novel biomarker of clinical utility to be identified. The handful of biomarkers that have successfully reached the clinic were identified mostly through retrospective analysis of archival formalin-fixed paraffin embedded (FFPE) biospecimens. The current gold standard for detecting proteins in FFPE tissues is immunohistochemistry (IHC), but this technology is wholly inadequate to support large-scale testing of hundreds of candidate biomarkers in retrospective validation studies, due to the high costs and long lead time for the development and analytical validation of new IHC assays. Furthermore, even with multi-parameter fluorescence detection, the multiplex capabilities of IHC remain limited and would only allow testing of small numbers of candidate biomarkers in each assay. Additionally, multiple sources of variation in IHC-based clinical assays have resulted in poor inter-laboratory concordance. Furthermore, as currently deployed, IHC assay results are semi-quantitative at best, leading to difficulties interpreting intermediate results, and hampering the ability to assemble multivariate panels as diagnostics. An emerging technology that has the potential to overcome this barrier is a targeted form of mass spectrometry called multiple reaction monitoring mass spectrometry (MRM-MS). While MRM enables specific, precise quantification of polypeptides at high multiplex levels, sensitivity is limiting for many analytes. To address thi limitation, we have developed a novel platform that couples peptide immuno-affinity enrichment to MRM, resulting in highly sensitive immuno-MRM assays. We recently established the feasibility of using this emerging immuno-MRM technology for large-scale testing of cancer biomarker candidates in plasma, and in this application we will perform advanced development of the immuno-MRM technology platform for application to small numbers of human cells derived from FFPE tissues.
In Aim 1, a standard operating procedure will be developed that supports analytically robust multiplex MRM and immuno-MRM quantification in FFPE cancer tissues.
In Aim 2, analytical validation of the immuno-MRM technology will be performed in an emulated retrospective biomarker validation study using archived human breast cancer tissues.

Public Health Relevance

To develop more effective and less toxic drugs for treating cancer, we need to develop new laboratory tests that can be run on cancer biopsies and used to determine the best specific treatment for each individual patient. Currently, we do not have adequate technologies to efficiently develop these new diagnostic tests. The goal of this application is to develop a new technology that will fill this void and enable us to identify new cancer lab tests much more efficiently.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Exploratory/Developmental Grants Phase II (R33)
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Special Emphasis Panel (ZCA1-SRLB-Q (M1))
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Mckee, Tawnya C
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Fred Hutchinson Cancer Research Center
United States
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Kennedy, Jacob J; Whiteaker, Jeffrey R; Schoenherr, Regine M et al. (2016) Optimized Protocol for Quantitative Multiple Reaction Monitoring-Based Proteomic Analysis of Formalin-Fixed, Paraffin-Embedded Tissues. J Proteome Res 15:2717-28