BAMS

The San Francisco Bay Area Mass Spectrometry (BAMS) discussion group

Tuesday, December13, 2005
6:00 pm to 9:00 pm

Hs Lordships Restaurant
Berkeley, CA

Dinner reservations required by noon on Friday December 9, 2005

Identification of Foodborne Pathogens by
Proteomic Analysis of Their Protein Biomarkers

Clifton “Keith” Fagerquist, Ph.D.
WRRC, ARS, USDA
Albany, CA

Abstract

The mass spectrometry/proteomics facility at the Western Regional Research Center, Agricultural Research Service, USDA (in Albany, California) is a multi-research unit supported facility which conducts fundamental and applied research in mass spectrometry and proteomics. My research in this facility is involved in the detection and identification of foodborne pathogens by analysis of protein biomarkers as well as understanding the effect of environmental conditions on pathogen protein expression. The impetus of the pathogen biomarker research originated with earlier work by Mr. Les Harden and Dr. Bill Haddon utilizing matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) of bacterial cell lysates for rapid pathogen identification. Using this simple and rapid technique, it is possible to identify the genus, species and, in some cases, the strain of a pathogen from the 10 to 20 protein biomarkers which appear in the mass spectrum. This technique can also detect the presence of "mixed" cultures which often complicate or confound analysis by other microbiological and molecular biological identification techniques. Currently, we employ a relatively simple pattern recognition software algorithm, developed by a visiting co-op student Mr. Brandon Garbus (University of Pacific) and Mr. Les Harden, for classification of spectra.

A vulnerability of pathogen identification by pattern recognition analysis of mass spectra is that identification of reference strains still relies on some other microbiological or molecular biological technique. For this reason and others, we are also actively engaged in identifying pathogen protein biomarkers using a bioinformatics approach that exploits the increasing availability of microbial genomes. Pursuing this bioinformatics approach, we extracted and definitively identified a prominant ~10 kD protein biomarker observed in the MALDI-TOF-MS spectrum of cell lysates of strains of Campylobacter. jejuni, C. coli, C. lari, C. upsaliensis, C. helveticus and C. concisus. The biomarker was identified as the DNA-binding protein: HU. It was observed that variations in HU m/z among species and strains were due to amino acid substitutions caused by non-synonomous mutations of the HU gene and not due to variations in post-translational modifications (PTMs). We have extended our proteomic identification to other prominent protein biomarkers and observed unexpected PTMs. The number and variety of PTMs detected in this relatively small number of biomarkers suggest that future bioinformatics algorithms for pathogen identification from their protein biomarkers will need to incorporate many more PTMs than previously thought.

Background

Dr. Clifton "Keith" Fagerquist received his Ph.D. in physical chemistry in 1994 under the direction of laser spectroscopist Professor Mostafa A. El-Sayed at UCLA where he studied stable and metastable metal/metal halide gas phase clusters using sector-field mass spectrometry and "link" scanning techniques. After post-doctoral FTMS research with Evan Williams at UC Berkeley, he studied the analytical factors which affect mass isotopomer measurements of metabolically important bio-molecules under Professor Marc Hellerstein also at UC Berkeley. In 1999, he became Director of the Mass Spectrometry Facility and Research Associate at the Department of Chemistry, University of Minnesota, Minneapolis. Two years later, he joined the Agricultural Research Service (ARS), Eastern Regional Research Center (in Wyndmoor, Pennsylvania) as a research chemist developing methods for the detection of chemical residues in tissues using LC/MS/MS. He then moved to the ARS, Western Regional Research Center (in Albany, California) where he is currently studying foodborne pathogens using mass spectrometry and proteomics. He is the author (or co-author) of over 30 publications and presentations on fundamentals and applications of mass spectrometry.

*Note: 2005 dues need to be paid to obtain member price. Dues ($30.00) may be paid while registering for dinner. If you are unsure of your 2005 Membership status, please email Carol Soppe.

Did you see or hear about the BAMS talk by Professor Murayama entitled "What is Mass?" What is it we are measuring after all? Check it out! Go to ctp.berkeley.edu and click on "Popular Talks & Articles" for a QuickTime file.

As a trial service to our members, we are now posting Situations Wanted. (Note: BAMS isn't a career center and will only post brief positions wanted for BAMS members only).

The San Francisco Bay Area Mass Spectrometry discussion group was formed in 1980 to provide a regular gathering for people interested in mass spectrometry and allied topics. BAMS currently has a membership of about 280 individual and 20 corporate members, and meets 8-10 times per year for a midweek dinner and lecture. Meetings attract between 30 and 90 people, and are held at a restaurant or hotel in the bay area convenient for our speaker. We usually convene at 6:00 pm for cocktails, dinner at 7:00 pm, and lecture at 8:15 pm.

If you have suggestions for a meeting topic, or know of a prominent mass spectrometrist who will be visiting the bay area, please contact our program chair.

To become a member, please fill out and mail in a membership form.
BAMS has been fortunate to have had many excellent speakers in our short history.
If you have suggestions for a meeting topic please contact our program chair.
If you have questions or comments about BAMS, please contact one of the BAMS officers.
Please thank our corporate sponsors who help keep BAMS membership and dinner costs low.
Here are some internet links that may be of interest to BAMS members.

If you have comments or suggestions for this web site, please email me at hugh-gregg@llnl.gov

Date:	Tuesday	Tuesday December 13, 2005
Time:	6:00 pm	Social hour, registration (no-host cocktails)
	7:00 pm	Dinner
	8:00 pm	Lecture
Dinner:	featuring:	Filet Mignon (Medium) topped with a Mushroom Crown
		Baked Salmon with lemon Buerre Bankc Sauce
		Vegetarian Dinner
	includes:	Side dishes, dessert, Coffee/Tea
Cost:	$30	BAMS members.
	$40	Non-members.
	$60	BAMS membership plus dinner cost
	$15	Students only.
	$300	2005 Corporate Sponsors
		Dinner reservations required by noon on Friday December 9, 2005