SGMS Meeting 2000

Mass spectrometry in protein studies from genome to function

Peter Roepstorff
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense University, DK 5230 Odense M, Denmark

The advances in DNA-sequencing and rapidly increasing amount of genome sequence data becoming available have changed the scope of protein analysis. Databases now provide the sequence of more than 400,000 proteins and this number is rapidly increasing. Consequently, the amino acid sequence of a protein of interest is likely to be available in a database. Sequencing of complete genomes gives rise to number of questions: "Which of the genes are expressed in the organism?", or if the organism is a higher eucaryote, "which genes are expressed in which cell types?" The complete 2D-PAGE map of the proteins expressed in a given cell type has recently been termed the "proteome" (1). Once a protein is identified as being interesting, then the next questions are: "Is this protein known?", "Does this protein contain secondary modifications, and if so, which and where?" , and "What is its function?"

We have attempted to develop fast, sensitive and highly specific tools based on combining PAGE, mass spectrometry and sequence information in databases (2). Examples taken from our recent research will include mass spectrometric identification of the proteins in 2D-gels and determination of secondary modifications in the identified proteins. Finally the future perspectives for extending mass spectrometric analysis to studies of higher order structures and protein interaction will be outlined.

(1) Wilkins, M.R. et al. (1996) Bio/Technology, 14, 61-65.

(2) Jensen, O.N., Larsen M.R., and Roepstorff P. (1998) Proteins: Structure, Function and Genetics 999 (Supl 2) 74-89.