An Integrated View of Bioinformatics for both Genomics and Proteomics

William S. Hancock,
Agilent Laboratories, Palo Alto, CA

The relationship of functional genomics to proteomics will be a key issue in the post-genome era. Functional genomics will be based on the study of the transcription/translation process and thus is a measure of the functionality of a given genome.  The term proteome has been introduced to define the full complement of proteins in a cell and thus requires description of the localization, concentration and multi-subunit associations of each of these proteins. Another requirement is the definition of the post-translational modifications such as glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components. These modifications often play a key role in the activity, localization and turnover of an individual protein species.  Such measurements have become even more challenging with the recent revolution in sequencing of the human genome that will result in the discovery of several hundred novel protein sequences of unknown function.  Thus the field of proteomics will require the development of a new set of analytical tools that allow the resolution and characterization of complex sets of protein mixtures in a high throughput manner.  This presentation will describe the development of new instrumentation aimed at this challenge, such as high efficiency separations coupled with mass spectrometry.  The presentation will also focus on strategies for integration of both genomic and proteomic data in the context of the biological system.