An oft-heard complaint in R&D is that technology can’t keep up with the concepts that scientists are trying to prove or disprove. “In the case of biomarkers, having the technology is simply not the problem,” says Daniel Chelsky, Ph.D, CSO of Caprion Proteomics. “In the last five years, mass spec has improved a bit, but only by about an order of magnitude in sensitivity. The technology is there, but most labs are not using it to its full potential.”
According to Dr. Chelsky, we will be hearing a lot more about mass spec-based proteomics because the field has matured to the point where it can now have a significant impact on drug discovery, from both the perspective of discovering new markers and validating candidate markers.
At “Biomarker World Congress” to be held in Philadelphia next month, presenters will talk about advances in the field, and also consider the perks and pitfalls as biomarker validation finds its way to standardization.
Caprion has implemented three new tools geared to improve the success rate of biomarker identification. “Our main focus is on the use of multiple reaction monitoring,” says Dr. Chelsky. “MRM allows you to multiplex up to 100 peptide candidates at a time, getting a very quantitative and convincing assessment and verification of candidate markers with speed, accuracy, reliability, and without the expense associated with discovery. This is why people are looking at MRM as the next step in mass spec-based proteomics and biomarker validation.”
This approach can also be used for specific proteins. “Recently, a company told us that the sensitivity of its ELISA was not sufficient. In two weeks, we were able to develop an MRM assay using an antibody pull-down that could quantify their protein at 1 ng/mL in plasma. We can go much lower with small proteins and peptides, even without antibody pull-downs. The other advantage of MRM is its specificity that antibodies alone can’t match.”
And the lower abundance proteins are where the most interesting findings are. Dr. Chelsky notes that researchers have become more selective. As a result, Caprion has developed a way to examine secreted proteins by isolating golgi and secretory vesicles, breaking them open, and comparing the contents under different conditions.
“We’ll look at diseased versus healthy, or treated versus untreated, and what we see in the ‘secretome’ will mimic what we later find in the blood. The advantage is that, when we isolate proteins straight from cells or tissues, they are highly concentrated and you know where they came from. We’ve been particularly successful with cancer because we have been able to get fresh human tumor tissue, especially in metabolic disease where people have been quite willing to give up some of their visceral and subcutaneous fat.”
Depletion columns mark another difference. These columns can deplete the high and moderately abundant proteins in plasma, removing between 95% and 99% of the total protein, resulting in a 20-fold minimum improvement in sensitivity. “But proteins that are not normally present in plasma are also found after using these columns. These tend to be the ones that are most interesting and now there is a way of detecting them,” Dr. Chelsky adds.