Productive relationships must be forged between disparate technology platforms and between technological, medical/biological, and statistical specialties. The U.S. National Cancer Institute is attempting to create a nucleus for this new approach in its Clinical Proteomic Technology Assessment for Cancer program within the broader Clinical Proteomic Technologies for Cancer initiative.
Beginning with a critical evaluation of existing technology and methods, the CPTAC teams have designed and carried out true multisite reproducibility studies of both approaches: shotgun unbiased discovery and targeted MRM assays. The results, recently presented and now submitted for publication, are revealing.
As has been expected based on earlier, less well-controlled studies (e.g., the HUPO plasma proteome exercise), the shotgun approaches produce a statistical samples of of the peptides in the proteome under study and thus often show significant differences in the sets of peptides from run to run both within and between laboratories (with greater similarity at the protein level).
The need for replicate runs to approach asymptotic completeness in proteome coverage is thus an inherent statistical feature of the method. The targeted MRM assays, on the other hand, derived from a widely used accurate quantitation approach for small molecules, can yield results that are accurate, reproducible (in this case across eight sites), and of wide dynamic range provided we restrict attention to a set of up to several hundred prespecified peptides.
These studies have confirmed the roles and fitness of these two approaches for discovery and verification of candidates in the biomarker pipeline, and provide confidence that both can be practiced effectively in multiple laboratories.
In parallel, it appears that MS-based measurements can deliver high-quality results in clinical laboratories as well. A specific example highlighting these issues is the clinical assay for plasma thyroglobulin, a thyroid-specific protein used to detect recurrence of thyroid cancer in patients whose diseased thyroids have been removed.
Andrew Hoofnagle, M.D., Ph.D., recently demonstrated an MS-based SISCAPA assay for peptides from thyroglobulin designed to circumvent several well-known and high-prevalence interferences plaguing the existing commercial immunoassays for this protein.
The prospects for major progress in protein biomarkers in readily accessible bodily fluids thus appear considerably brighter than even a year or two ago. The clinical and economic value of early detection of diseases like cancer, COPD, or Alzheimer’s is so great that once a real biomarker pipeline is proven, and the odds shifted from no chance to merely long, a strong case exists for more equal emphasis on the development of biomarkers and drugs.