SGMS Meeting 2000

FTMS and Automation – how does that fit?

Gary Kruppa, Matthias Witt, Gökhan Baykut, Arnd Ingendoh
Bruker Daltonik GmbH, Bremen, Germany

Fourier Transform Mass Spectrometry (FTMS) is known for providing highest performance in terms of mass resolution and mass accuracy. In combination with MALDI and ESI it is the instrument of choice for the determination of the elemental composition for intact molecules. Therefore, the interest of using FTMS for industrial pharmaceutical applications, new areas like proteomics or in general for the analysis of complex mixtures in biological material.is strongly growing.

In proteomics, e.g., the specificity of mass spectrometric protein identification depends on the accuracy of peptide mass assignments. Using FTMS can greatly enhance protein identification, since fewer peptide masses are required to produce positive hits with high and confident scores. In addition, sensitivity increased over the last few years especially with MALDI and the use of "AnchorChip" targets, thus making FTMS usable for the fmol amounts typically present in proteomic samples.

New dissociation techniques like Infrared Multiphoton Dissociation (IRMPD) increase the speed for MS/MS. In IRMPD, the absorption of photons from a continuous wave 25 W CO₂ laser by the precursor ion leads to their dissociation. Thus, the use of a collision gas, which typically requires several seconds to evacuate, is precluded. This is advantageous for LC-MS/MS experiments where high data acquisition rates are critical for maintaining the chromatographic resolution. Automated LC-MS/MS combined with a mass accuracy in the 2 ppm range is now within reach.

For the use in pharmaceutical labs or in proteomics, a relatively high level of automation is required. Improvements for the control of MALDI and ESI in FTMS with regard to full computer control was the first step towards this direction. With the introduction of WinNT systems for FTMS and the appropriate software for LC/MS control, overnight analyses can be performed with FTMS. Main problems are connected currently to the data handling, since with mass resolutions in the range of ca. 50,000 the size of the ion chromatograms are in the high MB to low GB range. Automated post-processing routines like ion current filters or connections to database search algorithms are in preparation.

The present status of automated FTMS will be presented with regard to typical applications in the above mentioned areas.