W. Henry Benner and Joseph M. Jaklevic 
LBNL, MS: 70A-3363, 1 Cyclotron Road, Berkeley, CA 94720 
timofeye@everest.bim.anl.gov 

The development of new ion detectors for mass spectrometry is the focus of this project. Our recent developments of charge- and energy- sensitive ion detectors offer new ways to measure and manipulate individual DNA molecules. Charge detection mass spectrometry (CDMS), invented at LBNL, measures the molecular weight of DNA molecules larger than about 500 bp. Starting with electrospray ionization for generating highly charged DNA ions, CDMS measures the charge and velocity of individual ions in vacuum as they fly through a small metal tube. The mass distribution of the molecules in a sample is calculated from measurements made on a number of ions. Typically, only about 1000 ions are needed to produce a peak in a mass spectrum for each component in the sample. We have demonstrated that CDMS can be used to analyze mixtures of linear ssDNA and plasmid DNA in the 1 to 15 kbp range. The upper mass limit extends well beyond this range. WE will show how CDMS is well suited for rapidly measuring the size of DNA fragments generated in the course of sequence verification. Our estimates predict that optimized signal processing will provide a way to analyze about 200 ions per second with CDMS. At this rate, sequence verification performed on RE digests of BACs could be performed more rapidly than with pulsed-field gel separations. Since CDMS performs a nondestructive measurement on DNA ions, it opens the possibility for sorting individual molecular ions. A device has been designed for sorting individual ions into the wells of a microtiter plate for the purpose of performing single molecule studies. Our sorting device works similarly to a flow sorter but operates on the principe of selection based on ion mass. We have also developed an energy-sensitive ion detector called a superconducting-tunnel junction (STJ). Our STJ detector responds to the energy deposited by an impacting ion. This ion detector has helped to extend the efficiency for detecting high mass ions in applications related to time-of-flight mass spectrometry. Now that IR-MALDI appears capable of ionizing large DNA molecules, this detector will be used to detect DNA ions in sequencing ladders by means of IR-MALDI-MS. 

(This work was supported by the Director, Office of Energy Research, Office of Health and Environmental Research, Human Genome Program, U.S. Department of Energy under contract number DE-AC03-76SF00098.)