oa Development of a novel switchable CE-MS interface with predictive trajectories for high-throughput proteomics studies

The capillary electrophoresis (CE)-mass spectrometry (MS) interface is anticipated to have pivotal roles to play in biomarker discovery, elucidation and validation, and in diagnostics, as well as in drug discovery. We are developing a CE-MS system as the natural extension of our Label-Free Intrinsic Imaging (LFiI™) platform, allowing a large increase in analytical power.

One of the most powerful analytical tools in bio-analytical science applications is the mass spectrometer, allowing identification and extraordinary resolving power. However, this instrument too has shortcomings – it really needs a separation system ahead of it. Traditionally liquid chromatogaphy (LC) or 2D-gel separation have been coupled to MS with relative robustness. However LC techniques are not ideally suited to the analysis of biomolecules, with the use of denaturing solvents, expensive columns etc. while flat gel systems have serious shortcomings in sensitivity, reproducibility, dynamic range, quantification and throughput. These are largely overcome with capillary approaches, such as the Label Free Intrinsic Imaging system, the Peregrine, developed by deltaDOT Ltd of London.

The CE-MS interface being developed by deltaDOT QSTP (Qatar Science and Technology Park) will be based on our real-time pattern recognition known as ‘predictive trajectories’ (‘PT’) and biomolecular switching on the LFiI platform, to allow specific protein bands, selected ‘on the fly’, to be separated and quantified, before they undergo trypsin digestion, injection and full MS analysis in a Waters high-definition mass spectrometer (‘Synapt’). Such an interface considerably reduces the system noise by giving a switch opportunity to analyse selected bands of interest from the bulk of background buffer and highly concentrated proteins of low interest. Another significant advantage of such an approach would arise from a more coherent signal where peptide fragments of the same protein would elute together, as opposed to traditional liquid chromatography where any peptide fragments could come from any proteins from the sample, requiring heavy and slow analyses processing.

Based on work in our QSTP labs, we present preliminary data of analyses undertaken with partners in Qatar University on a range of proteomic targets and other analytes. We show how the unique combination of LFiI + PT + HDMS Q-Tof can provide a significant enhancement in analytical power.