Advances in Proteomic Technologies and Its Contribution to the Field of Cancer

Abstract

Systematic studies of the cancer genome have generated a wealth of knowledge in recent years. These studies have uncovered a number of new cancer genes not previously known to be causal targets in cancer. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies are not widely available for most cancers. Precision care plans still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics is continuing to make major strides in the discovery of fundamental biological processes as well as more recent transition into an assay platform capable of measuring hundreds of proteins in any biological system. As such, proteomics can translate basic science discoveries into the clinical practice of precision medicine. The proteomic field has progressed at a fast rate over the past five years in technology, breadth and depth of applications in all areas of the bioscience. Some of the previously experimental technical approaches are considered the gold standard today, and the community is now trying to come to terms with the volume and complexity of the data generated. Here I describe contribution of proteomics in general and biological mass spectrometry in particular to cancer research, as well as related major technical and conceptual developments in the field.

Figure 1

Discovery-based versus targeted proteomics workflows using mass spectrometry.

Figure 2

The assay bottleneck prevents potential protein diagnostics from becoming clinically useful.

Figure 3

The incorporation of verification step into the NCI-CPTC pipeline bridging discovery and qualification.

Figure 4

MRM-MS-based assay workflows (± immunoaffinity enrichment of proteins or peptides). SISCAPA workflow using proteolytic peptides as surrogates for their respective proteins, as illustrated in the top panel of the schematic, is a sensitive approach to measure protein concentrations using immunoaffinity enrichment of surrogate peptides prior to MRM-MS. To achieve quantitation of the targeted protein(s), they are digested to component peptides using an enzyme such as trypsin. A stable isotope standard (SIS, blue asterisk) is added to the sample at a known concentration for quantitative analysis. The selected peptides are then enriched using anti-peptide antibodies immobilized on a solid support. Following washing and elution from the anti-peptide antibody, the amount of surrogate peptide is measured relative to the stable isotope standard using targeted mass spectrometry. Alternatively, an assay can start with immunoaffinity enrichment of intact target proteins from biospecimens using an internal stable isotope-labeled protein standard (red asterisk, such as PSAQ approach) and an antibody, as illustrated in the bottom panel, followed by proteolysis and final quantitation of the target.

Figure 5

Increase in number of MRM publications in PubMed over the past decade.