The next Step: Exploring the Proteome:
Translation and Beyond

Protein identification by combining mass spectrometry and bioinformatics

John S. Cottrell, Matrix Science Ltd.


Abstract:

Several methods have been developed for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use MS/MS data from one or more peptides. Yet others combine mass data with amino acid sequence data.

Following a general introduction, the talk will focus on selected topics: the importance of scoring algorithms, the challenges posed by large scale, high throughput protein identification, and the issues associated with searching complete genomes using uninterpreted mass spectrometry data.

In the context of genomic data, these methods can provide primary experimental verification of predicted coding sequences, as well as the potential to identify novel coding sequences. This approach to gene mining is more laborious than purely computational methods, such as sequence alignment or exon prediction, but it has the advantage of being an orthogonal approach, capable of finding truly novel genes

Biographical sketch:

BSc (1976) and PhD (1979) from University College London.

Career has revolved around mass spectrometry and its application to the life sciences. Initially with Kratos, (now part of Shimadzu Corporation). Participated in the development of the continuous flow FAB LC/MS interface, inhomogeneous magnet technology, and the first commercial electro-optical imaging detector. Later with Finnigan, (now part of Thermo Electron). Principally working on the development of MALDI-TOF instruments, initially as R&D Manager and later as Managing Director of the UK based MALDI division.

In 1998, co-founded Matrix Science, a bioinformatics company focused on the development and marketing of software products for mass spectrometry and proteomics. The company is well known for its Mascot software for protein identification.

Contact Information

Matrix Science Ltd., 30 Harcourt Street, London W1H 4HT, UK.
Tel: +44 (0)20 7723 2142, Fax: +44 (0)20 7725 9360, Email: jcottrell@MatrixScience.com