SGMS Meeting 2000

Automated LC/MS/MS with an ion trap mass spectrometer – a promising tool in high throughput proteomics

Christoph Siethoff, Winfried Wagner-Redeker
Spectronex AG Basel, Rotterdamstrasse 21, 4002 Basel

After decoding of the human genome is completed proteomics clearly is the new challenge in life science today. It is assumed, that about 100´000 genes in the human genome translate into more than 1 Mio proteins. This number is even largely increased by posttranslational modifications. In order to understand the biological functions of these proteins, a vast amount of information must be collected, both qualitatively and quantitatively. The need for very high throughput analysis at femtomol level and below will dictate proteomics research in the years to come and it will have a dominant impact on instrumental and software development. Mass spectrometry is of great importance in this field since it yields the sensitivity, the specificity and the speed required. Even with LC-MS techniques more than 100 proteins/hour can already be identified today.

The talk describes a protocol for automated protein identification via HPLC/MS/MS and subsequent data base search by Turbosequest. It describes the experimental setup in our laboratory and gives examples which illustrate the type and amount of information generated.