Since its introduction a few years ago, the linear ion trap Orbitrap (LTQ Orbitrap) instrument has become a powerful tool in proteomics research. For high resolution mass spectrometry measurements ions are accumulated in the linear ion trap and passed on to the Orbitrap analyzer. Simultaneously with acquisition of this signal, the major peaks are isolated in turn, fragmented and recorded at high sensitivity in the linear ion trap, combining the strengths of both mass analyzer technologies. Here we describe a next generation LTQ Orbitrap system termed Velos, with significantly increased sensitivity and scan speed. This is achieved by a vacuum interface using a stacked ring radio frequency ion guide with 10-fold higher transfer efficiency in MS/MS mode and 3–5-fold in full scan spectra, by a dual pressure ion trap configuration, and by reduction of overhead times between scans. The first ion trap efficiently captures and fragments ions at relatively high pressure whereas the second ion trap realizes extremely fast scan speeds at reduced pressure. Ion injection times for MS/MS are predicted from full scans instead of performing automatic gain control scans. Together these improvements routinely enable acquisition of up to ten fragmentation spectra per second. Furthermore, an improved higher-energy collisional dissociation cell with increased ion extraction capabilities was implemented. Higher-collision energy dissociation with high mass accuracy Orbitrap readout is as sensitive as ion trap MS/MS scans in the previous generation of the instrument.

Liquid chromatography (LC) prefractionation is often implemented to increase proteomic coverage; however, while effective, this approach is laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described high-field asymmetric waveform ion mobility spectrometry (FAIMS) device between a nanoelectrospray ionization (nanoESI) emitter and an Orbitrap hybrid mass spectrometer (MS) enables the collection of single-shot proteomic data with comparable depth to that of conventional two-dimensional LC approaches. This next generation FAIMS device incorporates improved ion sampling at the ESI-FAIMS interface, increased electric field strength, and a helium-free ion transport gas. With fast internal compensation voltage (CV) stepping (25 ms/transition), multiple unique gas-phase fractions may be analyzed simultaneously over the course of an MS analysis. We have comprehensively demonstrated how this device performs for bottom-up proteomics experiments as well as characterized the effects of peptide charge state, mass loading, analysis time, and additional variables. We also offer recommendations for the number of CVs and which CVs to use for different lengths of experiments. Internal CV stepping experiments increase protein identifications from a single-shot experiment to >8000, from over 100 000 peptide identifications in as little as 5 h. In single-shot 4 h label-free quantitation (LFQ) experiments of a human cell line, we quantified 7818 proteins with FAIMS using intra-analysis CV switching compared to 6809 without FAIMS. Single-shot FAIMS results also compare favorably with LC fractionation experiments. A 6 h single-shot FAIMS experiment generates 8007 protein identifications, while four fractions analyzed for 1.5 h each produce 7776 protein identifications.

We establish a rigorous theoretical connection between measurements of the angular distribution of atomic photofragment alignment and the underlying dynamics of molecular photodissociation. We derive laboratory and molecular-frame angular momentum state multipoles as a function of photofragment recoil angles. These state multipoles are expressed in terms of alignment anisotropy parameters, which provide information on state symmetries, coherence effects, and nonadiabatic interactions. The method is intended for analysis of experimental data obtained with two-photon spectroscopy and ion imaging techniques, although it is readily modified for treating Doppler or time-of-flight mass spectrometer peak profiles. We have applied this method to the photodissociation of Cl2 at 355 nm, where we observe strong alignment in the ground state chlorine atom photofragments. Our analysis demonstrates that there are important contributions to the alignment from both incoherent and coherent perpendicular excitation. We also show that the existence of atomic alignment due to coherence requires that nonadiabatic transitions occur at long range.

High resolution ion imaging study of BrCl photolysis in the wavelength range 330-570 nm Quasiclassical and quantum mechanical modeling of the breakdown of the axial recoil approximation observed in the near threshold photolysis of IBr and Br 2The photodissociation of jet-cooled IBr molecules has been investigated at numerous excitation wavelengths in the range 440-685 nm using a state-of-art ion imaging spectrometer operating under optimal conditions for velocity mapping. Image analysis provides precise threshold energies for the ground, I( 2 P 3/2 )ϩBr( 2 P 3/2 ), and first excited ͓I( 2 P 3/2 )ϩBr( 2 P 1/2 )͔ dissociation asymptotes, the electronic branching into these two active product channels, and the recoil anisotropy of each set of products, as a function of excitation wavelength. Such experimental data have allowed mapping of the partial cross-sections for parallel ͑i.e., ⌬⍀ϭ0) and perpendicular ͑i.e., ⌬⍀ϭϮ1) absorptions and thus deconvolution of the separately measured ͑room temperature͒ parent absorption spectrum into contributions associated with excitation to the A 3 ⌸(1), B 3 ⌸(0 ϩ ) and 1 ⌸(1) excited states of IBr. Such analyses of the continuous absorption spectrum of IBr, taken together with previous spectroscopic data for the bound levels supported by the A and B state potentials, has allowed determination of the potential energy curves for, and ͑R independent͒ transition moments to, each of these excited states. Further wave packet calculations, which reproduce, quantitatively, the experimentally measured wavelength dependent product channel branching ratios and product recoil anisotropies, serve to confirm the accuracy of the excited state potential energy functions so derived and define the value ͑120 cm Ϫ1 ) of the strength of the coupling between the bound (B) and dissociative (Y ) diabatic states of 0 ϩ symmetry.

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