Biomarker discovery

Biomarker discovery

 

We have established and employed a mass spectrometry-based platform for the identification of potential biomarkers from plasma or other biofluids. To achieve this, high abundance proteins are depleted from plasma using immunoaffinity chromatography, allowing the identification of lower abundance proteins within the mass spectrometers. Another key feature of the workflow to increase proteomic penetration is the use of 2D liquid chromatography to fractionate the peptides. We are also investigating prefractionation of the proeins prior to their hydrolysis for mass spectrometry. Quantification of proteins is carried out using iTRAQ labelling; eight samples can be multiplexed in a single mass spectrometry run, saving time and cost. The technical and biological variation observed in experiments is low; with six samples per a group (eg. Pre-vs post- treatment) having been empirically calculated to provide enough statistical power to identify possible biomarkers. With the use of a reference pool multiple iTRAQ experiments can be directly compared allowing the analysis of sample sizes larger than a single ITRAQ experiment would allow. The combination of mass spectrometers available allow the complementary acquisition of data, for example via the use of both Matrix Associated Laser Desorption Ionisation (MALDI) and Electrospray Ionisation (ESI).