We propose to design, build and develop a compact tandem time-of-flight mass spectrometer for high throughput proteomics research based upon several technologies being developed in our laboratory. In particular the first mass analyzer (MSI) will utilize mass-correlated acceleration to focus ions with different kinetic energies and independently of mass to a focus point that is the entrance to the second mass analyzer (MS2). MS2 will be an endcap reflectron, which provides high order (nearly quadratic) kinetic energy focusing. The collision chamber will be located early on in the flight tube of MS1 as it is an essential feature of this instrument that there are no decelerating or re-accelerating fields, either constant or pulsed, between the ion source and the entrance to the endcap reflectron. Thus, fragment ions associated with a mass-selected precursor ion, and produced by collision-induced dissociation (CID) or by metastable decomposition, will be recorded at the same flight time. The high energy bandwidth endcap reflectron does not require stepping or scanning to record the entire product ion mass range in each time-of-flight cycle. In addition, because this reflectron also does not require reacceleration of after collision, it will be possible to utilize the full ion kinetic energy (10-20 keV) in collisional activation. The instrument will be utilized in a number of ongoing research projects involving peptidic and glycolipid antigens, the structures of lipid A, and protein arrays on a chip. In addition, a novel planar endcap reflectron design will be developed that is compatible with orthogonal acceleration. This will be used on an existing electron impact/orthogonal acceleration instrument, and will be further developed using atmospheric pressure MALDI as the ionization source. This technology is expected to bring high performance and tandem capabilities to a simple, compact instrument that can be utilized in proteomics research.
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