We use several mass spectrometers in the lab, a MALDI orthogonal time-of-flight mass spectrometer prOTOF (PerkinElmer), a MALDI ion trap mass spectrometer vMALDI-LTQ (Thermo Finnigan), and an electrospray QTRAP mass spectrometer (Sciex) coupled to a nano-HPLC system.
Modular Mass Spectrometric Tool
We combined two high-performance MALDI mass spectrometers, prOTOF and vMALDI-LTQ, into one mass spectrometric tool capable of providing fast, accurate, and sensitive analysis of complex biological samples.
The analysis of a typical sample starts with acquisition of a single-stage MS spectrum using the prOTOF instrument . This is a high sensitivity and high resolution device, which provides accurate, within 5-10 parts-per-million values of the masses of the detected species. Mass values extracted from the MS spectrum are used to generate an instrument control script for subsequent acquisition of fragmentation spectra from all species detect in the single-stage spectrum. The MALDI target is then transfered into the vMALDI-LTQ, an instrument optimized for very high sensitivity fragmentation analysis. This instrument is capable of fast , ~3 sec per spectrum, acquisition of MS/MS spectra in the single femtomole regime, allowing generation of 1200 spectra per hour. The successful analysis of complex peptide mixtures frequently depends on measurements of both high accuracy precursor ion masses and comprehensive fragmentation data. We achieve these properties through the combined use of two physically decoupled instruments, each optimized for a specific role. In combination, these spectrometers provide data containing 5-10 ppm accuracy in precursor mass measurement and informative fragmentation spectra while readily functioning in the single femtomole range and requiring only 2-3 seconds per MS/MS spectrum. An example illustrating the application of the modular MS tool for the analysis of the composition and phospnorylation of yeast anaphase promoting complex (APC) can be found in our publications.