The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science

Abstract

Better biomarkers are urgently needed to cancer detection, diagnosis, and prognosis. While the genomics community is making significant advances in understanding the molecular basis of disease, proteomics will delineate the functional units of a cell, proteins and their intricate interaction network and signaling pathways for the underlying disease. Great progress has been made to characterize thousands of proteins qualitatively and quantitatively in complex biological systems by utilizing multi-dimensional sample fractionation strategies, mass spectrometry and protein microarrays. Comparative/quantitative analysis of high-quality clinical biospecimen (e.g., tissue and biofluids) of human cancer proteome landscape has the potential to reveal protein/peptide biomarkers responsible for this disease by means of their altered levels of expression, post-translational modifications as well as different forms of protein variants. Despite technological advances in proteomics, major hurdles still exist in every step of the biomarker development pipeline. The National Cancer Institute's Clinical Proteomic Technologies for Cancer initiative (NCI-CPTC) has taken a critical step to close the gap between biomarker discovery and qualification by introducing a pre-clinical "verification" stage in the pipeline, partnering with clinical laboratory organizations to develop and implement common standards, and developing regulatory science documents with the US Food and Drug Administration to educate the proteomics community on analytical evaluation requirements for multiplex assays in order to ensure the safety and effectiveness of these tests for their intended use.

Fig. 1

Barriers between candidate biomarker discovery by proteomics and qualification.

Fig. 2

The envisioned National Cancer Institute-Clinical Proteomic Technologies for Cancer initiative (NCI-CPTC) development pipeline from discovery to qualification. (A) The gap in the current proteomics research pipeline. (B) The incorporation of verification into the NCI-CPTC pipeline between discovery and qualification.

Fig. 3

Multiple Reaction Monitoring Mass Spectrometry (MRM-MS). A schematic of a triple quadrupole mass spectrometer (QQQ-MS) commonly used in MRM-MS analysis: Q1 and Q3 represent two mass filters for precursor and fragment ion selection while Q2 (collision cell) creates fragment ions via collisionally-induced dissociation (CID). In this case, one of the three peptide precursor ions (colored in blue) is selected in Q1, fragmented in Q2 and quantitated using one of its fragment ions (transition) selected in Q3 by the relative intensity of its peak area. An MRM-MS assay offers multiplexing capability of many target analytes in a single HPLC run.

Fig. 4

Regulatory science education through the development of public documents that enable a more efficient flow through biomarker discovery, development and regulatory processes.

Fig. 5

National Cancer Institute-Clinical Proteomic Technologies for Cancer initiative proposed proteomics development and implementation process.