Abstract
High throughput proteomics is one of the buzzwords of the post-genome research.  Ideally the protein content of cells should be separated, visualized, quantitated, digested, extracted, analyzed and identified in an automated way, controlled by computers, without human interference.  My specialty is sequencing peptides by mass spectrometry.  In my talk I will present some of the unexpected peptides, cleavages, modifications, impurities I have found in my not too long tenure in proteomics, that make protein identification challenging. The very same measures used to enrich the proteins of interest in the preparation or keep the samples clean may introduce new impurities.  Everybody knows about potential problems in immunprecipitation, but did you know, that the side chain-blocked trypsin is not as "innocent" as we want to believe?  Similarly, one has to discover that latex gloves are not made of plastic.  One frequent reason for failing to identify a protein is that the mature form of proteins and the database entries usually are not the same.  Covalent modification of the amino acids during the isolation process - Cys and Met are the main culprits - may also contribute to the confusion.  For the projects discussed I used MALDI (AB DE-STR), and nanospray or automated nanoLC/MS/MS on a quadrupole-oa-TOF instrument (QSTAR).  I believe most of you involved in this field may find my observations useful.

Background
I got my diploma as a chemist, as well as my Ph.D. in peptide synthesis at the Eotvos Lorand University in Budapest, Hungary.  I worked on the structure - biological activity relationship of enkephalins.  I became involved with mass spectrometry while working at Gedeon Richter Ltd, a pharmaceutical company, also in Budapest, Hungary.  There I mostly analyzed small heterocycles, steroids and alkaloids using EI.

I started to work at UCSF as a visiting postdoc in 1988. The head of the MS Facility and my boss is Prof. Al Burlingame.  I happened to be the first in this laboratory who sequenced a protein, a fatty acid-binding protein from shark liver, from high energy CID data.  Peptide fragmentation in all kind of MS/MS experiments is still my specialty.  However, I have characterized a wide variety of posttranslational modifications of proteins, such as phosphorylation, disulfide bridges, N- and O-glycosylation, covalent cofactors, as well as chemical modifications introduced to gain information on the tertiary structure or the active site of an enzyme.

I have just started my own proteomics group, the first in my country, in the Biological Research Center of the Hungarian Academy of Sciences, in Szeged, Hungary.
 

Meeting details

Date:	Wednesday	June 20, 2001
Time:	6:00 pm	Social hour, registration (no-host cocktails)
	7:00 pm	Dinner
	8:15 pm	Presentation (free, no reservations required)
Dinner:	Choice of:	Chicken Parmegiana
		Eggplant Parmegiana
	includes	Caesar salad, fresh vegetables, pasta, ice cream, coffee, and wine
Cost:	$25.00	BAMS members.  Reservations required by noon on Friday June 15, 2001
	$35.00	Non-members.  Reservations required by noon on Friday June 15, 2001
	$15.00	Students only.  Reservations required by noon on Friday June 15, 2001

Note: 2001 dues need to be paid to obtain member price.  Dues ($20) may be paid at the meeting

Maps & directions
Francesco's
8520 Pardee Drive at Hegenberger Road, Oakland, CA 94621
(510) 569-0653
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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 6:00pm for cocktails, dinner at 7:00pm, and lecture at 8:15pm.

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Last update: 6/7/01.