The Approach and Design of a Surrogate Protease Substrate for Disease Biomarker Discovery

Biomarker discovery investigations utilizing sera samples typically show differences in peptides originating from high abundant proteins. These peptides, produced from the activity of one or more protease(s), by themselves may not reflect a disease-associated biomarker(s), but in fact, show the downstream effect of disease specific protease(s). The ability to select “true” biomarkers of disease is mired by the inter- and intrapatient variability typically observed in a proteomics approach to serum biomarker discovery. As an example, serum from an individual was collected with three types of serum separator tubes (SST) and stored at 4°C for prolonged periods of time. The postcollection integrity of the serum was examined using microcapillary nanoflow reversed-phase liquid chromatography (nano-RPLC) tandem mass spectrometry (MS/MS) of the trypsin-digested, low molecular weight protein fraction. An increase in unique peptides per protein was observed for the highest abundant proteins with prolonged storage t...