Ian Shadforth

Supervisor: Dr. Conrad Bessant

School: Institute of BioScience & Technology, CCBIT at Cranfield University.

The focus of the EngD project, in collaboration with GlaxoSmithKline (GSK), is to develop a system to enable high-throughput processing of proteomic mass-spectra. Current production of proteomic MS and tandem MS data far exceeds our analytical capacity and so individuals choose to analyse the mass-spectra of interesting sets of peptide fragments – a tiny proportion of the available data. GSK uses a commercially licensed program, Mascot, to match spectra against a database of known and predicted proteins, however around 50% of peptide fragments remain unassigned to proteins after Mascot processing. Hidden in this information are likely to be as yet undiscovered proteins and variants of currently known proteins.

A strategy and system for processing such information to yield the maximum benefits in terms of generation and accessibility of knowledge is being developed. The existing Mascot program alongside orthogonal algorithms, such as ProbID, will form the core of the high-throughput processing system. Not only must the system accurately identify peptide fragments or their origin, but also must provide chains of evidence for the assignations made. These will allow researchers to quickly form a view as to the veracity of an assignation before performing further work based upon it.

Work modules currently being progressed are:

1. Pre-processing of data files to appropriate formats for analysis
2. Batching of Mascot and ProbID processes
3. Development of strategies and programs to meaningfully combine output data

The output from this project will represent a significant increase in our knowledge of proteins produced by the genes of human, mouse and rat; although in principle data from any species may be considered.