Detecting Protein Changes
Merck & Co’s(www.merck.com) proteomics research group is using high-resolution MS to identify and quantify changes in peptide and protein levels related to disease or therapeutic agents.
“Our goal is to facilitate Merck’s basic research and to impact clinical medicine by providing a scientific approach to address these questions without antibody reagents,” states Ronald Hendrickson, Ph.D., director of proteomics, molecular profiling, Merck Research Labs (www.merck.com/mrl). A main advantage to this approach is the ability to perform unbiased analyses in complex biological systems without having to prespecify the analyte being measured, adds Dr. Hendrickson.
Since MS can rapidly cross species boundaries, it enables quick movement from cell-based experiments to preclinical models and then to humans. Dr. Hendrickson’s lab utilizes a triple quadrupole MS-based assay that uses stable isotope-labeled internal standards to improve precision and provide absolute quantification in lieu of developing an ELISA assay, which is time limiting.
The group is currently focusing on peptide and protein markers of proximal target engagement. This class of markers helps to address the question “did treatment engage the desired biochemical target?” Knowing this information in both preclinical models and human trials is critical and can help inform early go or no-go decisions. Another interesting application involving this type of MS is looking at protein turnover rates, where an understanding of protein dynamics is especially important to some diseases.
Key characteristics to look for in a MS system, says Dr. Hendrickson, include resolution, mass accuracy, sensitivity, dynamic range, and compatibility with the chromatography timescale. “I look for instruments that can maintain mass accuracy of better than five parts per million over a three-week period without requiring recalibration and without an internal standard.”