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British Society for Proteome Research

The first meeting of the British Society for Proteome Research (BSPR) was held at the European Bioinformatics Institute in Hinxton, UK, on July 12th and 13th, 2004. In the inaugural speech, Mike Dunn, President of BSPR (formerly the British Electrophoresis Society), explained that renaming the society was driven by recent developments in genomics and postgenomic activities, which required recognition of the focus on protein research that the electrophoresis society had largely been engaged with. The theme of the inaugural meeting was functional proteomics and was held over 2 days and divided into four sessions. The speakers were largely from research institutes and universities in the UK, and three from outside (Fred Regnier and Leigh Anderson from the USA and Peter James from Sweden). The presentations were understandably biased towards academic research groups. It was clear that the broad definition of proteomics as the qualitative and quantitative identification of protein composition continues to remain strongly positioned as the fundamental methodology. Taking a high-level view of the conference presentations, one could identify some very specific developments and applications from fundamental analysis on the global proteome in various systems, protein localization studies within the cell, elucidation of metabolic changes and pathway analysis and finally to methods and technology developments. Compartmentalization of proteomic research efforts into specific areas is difficult due to the hazy demarcating boundaries between them and the variety of interlinks connecting them. Furthermore, a range of traditional and novel technologies span these broad themes. The first speaker of the conference was Janet Thornton (European Bioinformatics Institute [EBI]), who presented work in structural proteomics, starting with an overview of the large European Genomics and Proteomics Initiatives including the Oxford Protein Production Group, with EBI in Cambridge and the Protein Structural Facilities in Germany. Thornton’s group at the EBI in the UK is specifically focused on structure-to-function annotation, particularly where there is less than 30% homology. Approximately 60 such structures have been identified of which one third are hypothetical (i.e., have no identified functions associated as yet). However, Thornton emphasized that knowing the structure is not always sufficient for function elucidation pointing to a specific type of triosephophate isomerase barrel that can be seen in over 60 different types of enzymes. Identifying ligand and substrate binding site from the structure is an approach for function determination and such predictions can be based on comparison of the surface cleft, residue conservation and through the use of specific structural motifs. An alternate approach is the use of crystal structure for protein–protein interactions, although discriminating between monomers and homodimers was important to obtain a nonredundant data set. David Harvey (University of Oxford, UK) also discussed structural elucidation of proteins in an interesting presentation on the analysis of carbohydrate groups attached to proteins. A number of approaches for analyzing glycosylated proteins were highlighted, including trypsin digestion, enzymatic removal of specific carbohydrate residues as well as collision-induced fragmentation. Global proteome analysis is an implicit starting point for most proteomic research applications. A very comprehensive study of the human plasma proteome was presented by Leigh Anderson, Director of the Plasma Proteome Institute (WA, USA). Anderson began by asking three key questions: