Dawn M. Maynard National Human Genome Research Institute, NIH Office: 301-402-6622 FAX: E-mail: maynardd@mail.nih.gov Job Title: Staff Scientist Ph.D. in Analytical Chemistry from Texas A&M University, College Station, TX

Speaker: Dawn M. Maynard, Laboratory of Neurotoxicology, NIMH, and Molecular Genetics Branch, NHGRI, Bethesda, MD 20894

Topic: Evaluation of an Automated Multi-dimensional LC-MS/MS System and Data Parsing Program for Proteomics

Place: Building 549, Auditorium, NCI at Frederick, Frederick, MD

Time: Tuesday, February 10, 2004, at 2:00 PM

Abstract: A rugged, reproducible, multi-dimensional LC-MS/MS system was developed to identify and characterize proteins involved in protein-protein interactions and protein complexes. This system employs SCX in the first dimension and RP in the second dimension and is built from Shimadzu LC-VP Series components connected directly to a ThermoFinnigan LCQ Classic ion trap mass spectrometer. In order to evaluate the performance and reproducibility of this multi-dimensional LC-MS/MS system, peptides obtained from sequential yeast extracts were used as a model system. A program called DBParser was developed to process and evaluate the large 2D-LC-MS/MS data sets that resulted. DBParser takes Mascot results and loads them into a relational database for subsequent sorting and comparison. As an example, a comparison of two yeast files (10,000 .dta files each) from Mascot required just seconds to sort into lists identifying proteins unique to each analysis.