Workshop I: High Throughput Technologies and Methods of Analysis

March 22 - 26, 2004

Overview

Focus: new technologies such as mass spectrometry and protein arrays and methods of analysis, both analysis of experiments and analysis leading to an understanding of protein networks.

The workhorse of proteomics is 2-D gel electrophoresis. This technology spreads out proteins in a sample differentially in the plane, producing a collection of spots, each of which contains one protein. A comparatively new technology has come on line — mass spectrometry — that promises to be to proteomics what automated sequencing machines were to genomics. The basic modality is protein mass fingerprinting — a protein is cut into segments and then the fragment masses measured very precisely using mass spec. By comparison with protein databases, the composition of the fragments can be determined, and from this the entire protein reconstructed.

There are numerous challenges to making this an effective high-throughput method. Mass spec facilities are springing up at research facilities worldwide. In addition, there are a number of new technologies coming on line that will provide even more information. Each technology raises interesting issues of analysis, ranging from comparatively familiar issues of image analysis to the much more open issues of how to use the information generated to reconstruct networks of protein interactions.

Other new technologies that hold great promise—for example, Protein Chips/ microarrays, Yeast Two-hybrid Assays and Coimmunoprecipitation-2D Gel-Mass Spec – will also will be included here.

This workshop would include representatives from companies with products for mass spec and other high-throughput proteomics methods, and researchers who are users of these technologies and those engaged in the analysis of data generated by these technologies.

Organizing Committee

Vineet Bafna (University of California at San Diego, CSE)
Tim Ting Chen, Chair (University of Southern California, Program in Molecular and Computational Biology/CS/Math)
Joseph Loo (UCLA, Biochemistry & Chemistry)
Pavel Pevzner (University of California at San Diego, Computer Science and Engineering)