About Us
Proteogenomics is an exciting new research area that utilizes the whole genome MS/MS datasets to better characterize the genomic and proteomic annotations on a global scale. In comparative proteogenomics, we explore how such data from multiple related organisms can be exploited to obtain better anotations. The consortium provides an opportunity to the undergraduate and fresh graduate students to get hands-on research experience with real and unsolved bioinformatics problems in this upcoming field.
Here are some specific applications in which we are using comparative proteogenomics (this list is growing !):
- Correcting gene start sites
- Identification of frameshifts
- Detection of proteolytic sites in proteins
- Resolving one-hit-wonder proteins in mass spectrometry
- Analysis of pathways
- Peptide Detectability
- Post translational modifcation of proteins
Supported
By 
Whats New
Trypsin paper accepted
"Does Trypsin cut Before Proline?" paper with our undergraduate student Jesse Rodriguez as the first author has been accepted for publication in the Journal of Proteome Research. Congratualtions Jesse!
Consortium alumni
Jesse Rodriguez joins Stanford, Noah Ollikainen joins UCSF and Ian Kerman joins UCSD for graduate studies. Congratulations to all!
Comparative analysis paper
The first draft of of the paper summarizing results of all students on
using comparative approaches for analyzing MS/MS data is completed. It
will be submitted for publication shortly.
Poster at ASMS
Jesse Rodriguez presented a poster on his work on analyzing trypsin specificity at ASMS 2007 in Indianapolis to thousands of mass-spectrometry experts.
HHMI site visit
Mary
Koszalka from HHMI visited us, and learnt about the consortium projects
through presentations made by Jamal Benhamida, Jesse Rodriguez and
Nitin Gupta.
Collaborators
University of California, San Diego
Pacific Northwest National Laboratory
Burnham Institute
Howard Hughes Medical Institute