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University of Saskatchewan, Department of Computer Science

2002-2003 Seminar Series

Proteomics, Mass Spectrometry, Data Analysis Algorithms and all that...

Andrew Robinson
Oxford Glycosciences

DEPARTMENT SEMINAR
DATE: Monday, October 7, 2002
TIME: 3:30 p.m.
PLACE: Engineering 2C40
*** Everyone is welcome ***

Abstract

Large scale, high throughput proteomics operations, which rely on the interpretation of very large numbers of mass spectra without human intervention, pose considerable challenges in both data interpretation algorithm and process flow design. At OGS we generate many thousands of mass spectra per day, far beyond the capacity for human inspection of each result. The data processing system used at OGS requires the integration of two sets of mass spectrometry results, MALDI (matrix assisted laser desorption ionisation) and tandem (or MS-MS) mass spectrometry. I will outline data algorithms for peak picking from mass spectrometry data (which are also generally applicable across a range of scientific data), de-Novo peptide sequencing from MS-MS spectra, searching large peptide databases and mapping results onto protein sequences. In addition I will discuss the process flow, and software, hardware and commercial factors in the design of the information processing system.

About the speaker

Andrew has B.Sc. and MSc degrees in Chemical Physics and Physical Chemistry from Bristol University and a Ph.D. in Physical Chemistry from Bath University. His original research area was interactions of molecules at surfaces. As part of his research he wrote many data acquisition, data visualisation and modelling tools. After spending several years doing synchrotron based surface science experiments and nanoscale physics experiments, instrumentation development and software development, at Liverpool University and Birmingham University, he moved to Oxford Glycosciences, a company specialising in proteomics based on mass spectrometry. For the last two years he has been telecommuting, working in England for OGS, but living in Saskatoon. [an error occurred while processing this directive]