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Workshop 3: Computational Proteomics and Mass Spectrometry
(January 11-14, 2005)

Organizer: Vineet Bafna and Tim Ting Chen

Proteomics is defined as the study of the total protein complement of a cell. This broad definition covers a lot of ground, including, but not limited to protein identification and quantification in specific cellular environments, structural genomics and fold recognition, identification and characterization of functional domains, and finally, the networks defining the interactions of proteins with bio-molecules (proteins, DNA, etc.). With the sequencing of the genome, and subsequent identification of the parts list (the gene and their protein products), there is a renewed emphasis on studying the proteome.

In this workshop, we will focus on emerging technologies for probing the proteome, with two focal points. The first is the computational analysis of mass spectrometry data. Simply speaking, a mass spectrum is a collection of masses and (relative) intensities of charged molecules. The spectrum of mass fragments of a protein (or peptide) sequence form a fingerprint that can be used for identification and relative quantification. Post translational modifcations can be measured using characteristic shifts in the spectrum. Various computational issues arise in the analysis mass spectrometry data for protein identification and quantification.

The second focus is the analysis of protein function, with an emphasis on combining evidence from emerging high-throughput technologies. Many techniques have been developed to profile protein function directly and indirectly. For example, multiple alignments of evolutionary-conserved protein domains provide direct annotation of functions of a protein; gene expression profiles can be used to cluster proteins with similar functions; protein interactions show how proteins interact with one another to carry the necessary functions. In particular, a large amount of protein interactions have been generated recently by several large-scale techniques such as mass spectrometry, gene-knockout, and yeast two hybrid assays. These data together provide us with a global view of the protein netwrok inside the cell. Analysis of such networks is critical to understand the biological system at the molecular level.

The workshop will aim to bring together the leading researchers in these areas to describe the state of the art, and also to present problems that will challenge the next generation of Bioinformatics researchers.