MASStermind®

Low abundance protein biomarker discovery

The MASStermind^® discovery platform enables the identification and relative quantitation of proteins at the low to sub nanogram per mL level directly from complex biological samples including clinical plasma and serum. This represents at least a one hundred fold increase in sensitivity and a significant increase in proteome coverage compared with other unbiased discovery methods. Quantifying proteins in this concentration range is a prerequisite for the detection of proteins specific to disease or therapeutic intervention. This is supported by a number of in-house studies showing the identification of tissue-leakage, signaling and other proteins directly from clinical and pre-clinical plasma samples.

This impressive performance is achieved through the application of state of the art methods, including Pronota's core proprietary COFRADIC™ technology used in the MASStermind process to reduce sample complexity. COFRADIC operates by specifically selecting for N-terminal tryptic peptides for further separation, whereas all non terminal fragments are removed from the peptide mixture thereby significantly reducing sample complexity in comparison with other proteomic workflows. This signature peptide selection process is combined with other state of the art methods including depletion of abundant proteins, advanced separation sciences, a novel quantitation metholodology, high-end mass spectrometry and sophisticated in-house designed bioinformatics tools. Working together this unique combination of techniques allows Pronota scientists to probe the lower strata of the proteome in a recurrent, reproducible fashion.

The output of a typical MASStermind^® discovery program is a high quality list of biomarker candidates with levels of abundance correlating with the phenotype of interest. Protein identifications are obtained by tandem MS sequencing and careful matching with available databases using advanced in-house designed bioinformatics methods. Constellations of proteins and processed products can also be mapped onto biological pathways to provide insights into drug mechanism of action or disease pathophysiology.

In addition to its extensive experience of working with plasma Pronota has also analysed a wide variety of other sample types including cerebrospinal fluid, bronchoaveolar lavage fluid, tissues and cells.

This N-terminal peptide selection method is also highly useful for the selection and identification of cleavage fragments resulting from in vivo proteolytic cleavage of intact proteins. In pharmaceutical development this provides an elegant system for mapping the on- and off-target effects of protease inhibitor compounds.