Proteome coverage and peptide identification rates have historically advanced in line with improvements to the detection limits and acquisition rate of the mass spectrometer. For a linear ion trap/Orbitrap hybrid, the acquisition rate has been limited primarily by the duration of the ion accumulation and analysis steps. It is shown here that the spectral acquisition rate can be significantly improved through extensive parallelization of the acquisition process using a novel mass spectrometer incorporating quadrupole, Orbitrap, and linear trap analyzers. Further, these improvements to the acquisition rate continue to enhance proteome coverage and general experimental throughput.

No abstract

A MALDI source is interfaced to a modified LTQ Orbitrap XL instrument. This work gives insight into the MALDI source design and shows results obtained with the MALDI source coupled to an accurate mass, high-resolution hybrid mass spectrometer. MALDI-produced ions and fragment ions thereof produced in the mass spectrometer may be analyzed and detected by the Orbitrap analyzer at a maximum mass resolution of 100,000 (FWHM) at m/z 400 with high mass accuracy. An accuracy of Յ2 ppm is achieved by internal mass calibration using lock mass functionality; using external mass calibration, an accuracy of Յ3 ppm is routinely obtained. External mass calibration of the hybrid mass spectrometer is performed using a standard calibration mixture of different peptides and matrix components. Short temporal spread (ϳns) of ultraviolet (UV) lasers and the small spatial distribution of desorbed ions match the requirements for time of flight mass analysis. Significant advances in fast electronics (data acquisition, detectors, high voltage (HV) pulsers, data processing), ion optics design, and the use of delayed extraction method [4 -7] led to the development of research grade and commercial TOF mass analyzers, exhibiting both high mass resolution (RP ϳ 10,000ֈ20,000 at FWHM), mass accuracy (ϳdown to a few ppm), and also high sensitivity due to low transmission losses [8]. Axial TOF InstrumentationStill mass analysis required skilled choice of laser energy (normally slightly above threshold for MALDI ion production), use of internal or external standards for calibration placed into the sample or in close proximity to the sample, thermal stabilization, and elaborated sample preparation. Increased laser energy is experimentally proven to help generate more ions and improves statistics for low abundant peaks, but also normally is accompanied by degraded mass resolution, mass accuracy, and intense in-source fragmentation [9]. Moreover, even though axial TOF systems are capable of recording mass spectra in a wide mass range, it is impossible to achieve uniform mass resolution across the whole mass range because the optimum delay time is mass-dependent. One has to choose between peak mass resolution in a narrow mass range and lower mass resolution attainable over the broader mass range [10,11] or stitch composed mass spectrum from various segments at the expense of duty-cycle. Efforts to resolve mass-dependency limitation of the delayed extraction method were undertaken by different groups [12][13][14] but in addition to more complicated electronics, it makes calibration highly nonlinear, requiring the use of standards. Collisional Cooling InterfacesAnother approach taken is to avoid the direct coupling of MALDI sources to mass analyzers. Maintaining the sample plate at an elevated pressure (ranging from tens of mTorr to atmosphere) [15][16][17][18][19] allows the MALDI event to occur under conditions in which ions' internal degrees of freedom are thermalized before onset of in-source fragmentation [20,21]. Consequently, one may increase...

The multi-particle simulation program ITSIM version 4.0 takes advantage of the enhanced performance of the Windows 95 and NT operating systems in areas such as memory management, user friendliness, Ñexibility of graphics and speed, to investigate the motion of ions in the quadrupole ion trap. New features and capabilities signiÐcantly broaden its applicability. The simulation program can provide help in understanding fundamental aspects of ion trap mass spectrometry and both precede experiments and assist in directing their course. It also has didactic value in elucidating and allowing visualization of ion behavior under a variety of experimental conditions. ITSIM 4.0 provides easy access to ion simulations for all users through a dramatically improved user interface. The program uses the improved Euler method to calculate ion trajectories as a numerical solution to the Mathieu di †erential equation. The Windows version can simultaneously simulate the trajectories of ions with a virtually unlimited number of di †erent mass-to-charge ratios, up to a maximum of 600 000 ions, and hence allow realistic mass spectra, ion kinetic energy distributions, phase-of-ejection distributions and other experimentally measurable properties to be simulated. The simulated data are used to obtain mass spectra from mass-selective instability scans and by Fourier transformation of image currents induced by coherently moving ion clouds. Field inhomogeneities arising from exit holes, electrode misalignment, imperfect electrode surfaces or alternative trap geometries can be simulated with the program. Non-zero angle scattering in the hard-sphere collision model allows simulations involving collisional cooling to be performed. Complete instruments, from an ion source through the ion trap mass analyzer to a detector, can be simulated. Some typical applications of the simulation program are presented and discussed. Such features as the mass-selective instability scan mode, mass-range extension via resonant ion ejection, r.f. and d.c. ion isolation and non-destructive detection are shown. Comparisons are made between the simulated and experimental results, for example in mass-selective photodissociation. Fourier transform experiments and a novel six-electrode ion trap mass spectrometer illustrate cases in which simulations precede reduction to practice.

The multi‐particle simulation program ITSIM version 4.0 takes advantage of the enhanced performance of the Windows 95 and NT operating systems in areas such as memory management, user friendliness, flexibility of graphics and speed, to investigate the motion of ions in the quadrupole ion trap. New features and capabilities significantly broaden its applicability. The simulation program can provide help in understanding fundamental aspects of ion trap mass spectrometry and both precede experiments and assist in directing their course. It also has didactic value in elucidating and allowing visualization of ion behavior under a variety of experimental conditions. ITSIM 4.0 provides easy access to ion simulations for all users through a dramatically improved user interface. The program uses the improved Euler method to calculate ion trajectories as a numerical solution to the Mathieu differential equation. The Windows version can simultaneously simulate the trajectories of ions with a virtually unlimited number of different mass‐to‐charge ratios, up to a maximum of 600000 ions, and hence allow realistic mass spectra, ion kinetic energy distributions, phase‐of‐ejection distributions and other experimentally measurable properties to be simulated. The simulated data are used to obtain mass spectra from mass‐selective instability scans and by Fourier transformation of image currents induced by coherently moving ion clouds. Field inhomogeneities arising from exit holes, electrode misalignment, imperfect electrode surfaces or alternative trap geometries can be simulated with the program. Non‐zero angle scattering in the hard‐sphere collision model allows simulations involving collisional cooling to be performed. Complete instruments, from an ion source through the ion trap mass analyzer to a detector, can be simulated. Some typical applications of the simulation program are presented and discussed. Such features as the mass‐selective instability scan mode, mass‐range extension via resonant ion ejection, r.f. and d.c. ion isolation and non‐destructive detection are shown. Comparisons are made between the simulated and experimental results, for example in mass‐selective photodissociation. Fourier transform experiments and a novel six‐electrode ion trap mass spectrometer illustrate cases in which simulations precede reduction to practice. © 1998 John Wiley & Sons, Ltd.