Abstract
It is now well recognized that the sheer complexity and ever changing nature of the proteome necessitates the development of more powerful, higher-throughput analysis methods.  Although throughput can be increased simply by constructing parallel analysis systems, a more elegant approach involves the development of new integrated platforms within which all aspects of the analysis process from sample preparation to data analysis are chosen and optimized with respect to the other components in order to maximize the output of the overall system both in terms of the amount and quality of the data produced.  Here we describe a robust, highly automated analysis platform that effectively combines the flexibility and high peak capacity of multi-dimensional liquid chromatography with the high dynamic range and unsurpassed characterization power of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS).  A matrix-assisted laser desorption/ionization (MALDI) interface is employed to eliminate the experimental limitations imposed by online electrospray coupling.

Re-addressable records of thefinal reversed-phase separations are automatically produced using a novel deposition device that simultaneously deposits the effluents of multiple uHPLC columns onto surface-patterned MALDI targets through an electrically mediated process.  The sample concentration and localization provided by the hydrophobic/hydrophilic targets allow rugged automation of both the separation and the acquisition process.  Specifically, the concentration and localization of the deposited samples onto specific locations on the MALDI target plates allows uHPLC methods to be employed rather than the operationally more difficult nano-HPLC without a loss in sensitivity and also obviates the need for “sweet spot” searching during the MALDI process.  A unique lysine-specific labeling reagent enables differential quantitation while simultaneously preventing the reported dominance of arginine containing peptides in MALDI MS analyses, thus further increasing the amount of information obtained per analysis.

The sample plate is first automatically scanned in the MS mode only, the high dynamic range and exceptional mass accuracy of FT-ICR being maintained by true internal calibration of each spectra using a novel gas phase ion mixing scheme.  Data reduction and database searching are performed concomitantly using customized software programs.  The resulting monoisotopic masses, integrated intensities, and identifications based on accurate mass measurements and amino acid compositional information are stored in a database.  Tandem MS measurements can then automatically be performed as required based on user selected criteria applied to the MS output.  Data from the automated analysis of protein digests from both Thermotoga maritima and yeast are used to demonstrate the performance of the overall system.

Background
Ansgar Brock received his Diploma in Chemistry from the University of Karlsruhe, Germany and a Ph.D. in Physical Chemistry from Baylor University in 1996.  He worked as Postdoctoral associate at Stanford University from 1996-1999 with Professor Richard N. Zare on the development of Hadamard Transform TOF MS.  In 1999 Dr. Brock joined the newly founded Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, CA, where he is currently Group Leader of the Protein Profiling Group in the Protein Science Department.  His main responsibilities are in the areas of new technology development for proteomics and management of the support for a number of scientific projects at GNF and The Scripps Research Institute in La Jolla.  Research interests are in biotechnology, bioanalytical chemistry, separations/mass spectrometry, mass analyzer development, process automation.

Meeting details

Date:	Wednesday	January 23, 2003
Time:	6:00 pm	Social hour, registration (no-host cocktails)
	7:00 pm	Dinner
	8:00 pm	Lecture
Dinner:	Choice of:	Grilled Chicken baked with tomatoes, basil & jack cheese
		Petrale Sole stuffed with dungeness crab & shrimp in butter
		Stuffed Portabello Mushroom
	includes	(various side dishes & dessert)
Cost:	$25.00	BAMS members.  Reservations required by noon on Friday January 17, 2003
	$35.00	Non-members.  Reservations required by noon on Friday January 17, 2003
	$15.00	Students only.  Reservations required by noon on Friday January 17, 2003

Note: 2003 dues need to be paid to obtain member price.  Dues ($20) may be paid while registering for dinner.

Maps & directions
Dominic’s at Oyster Point
360 Oyster Point Boulevard
South San Francisco, CA  94080
(650) 589-1641
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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.

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Last update: 12/20/2002