Ion mobility–mass spectrometry: a new paradigm for proteomics

Matrix-assisted laser desorption/ionization (MALDI) coupled with ion mobility–mass spectrometry (IM–MS) provides a rapid (μs–ms) means for the two-dimensional (2D) separation of complex biological samples (e.g., peptides, oligonucleotides, glycoconjugates, lipids, etc.), elucidation of solvent-free secondary structural elements (e.g., helices, β-hairpins, random coils, etc.), rapid identification of post-translational modifications (e.g., phosphorylation, glycosylation, etc.) or ligation of small molecules, and simultaneous and comprehensive sequencing information of biopolymers. In IM–MS, protein-identification information is complemented by structural characterization data, which is difficult to obtain using conventional proteomic techniques. New avenues for enhancing the figures of merit (e.g., sensitivity, limits of detection, dynamic range, and analyte selectivity) and optimizing IM–MS experimental parameters are described in the context of deriving new information at the forefront of proteomics research.     

Kinetics of Surface-Induced Dissociation of N(CH3) 4 + and N(CD3) 4 + Using Silicon Nanoparticle Assisted Laser Desorption/Ionization and Laser Desorption/Ionization

The implementation of surface-induced dissociation (SID) to study the fast dissociation kinetics (sub-microsecond dissociation) of peptides in a MALDI TOF instrument has been reported previously. Silicon nanoparticle assisted laser desorption/ionization (SPALDI) now allows the study of small molecule dissociation kinetics for ions formed with low initial source internal energy and without MALDI matrix interference. The dissociation kinetics of N(CH₃)₄⁺ and N(CD₃)₄⁺ were chosen for investigation because the dissociation mechanisms of N(CH₃)₄⁺ have been studied extensively, providing well-characterized systems to investigate by collision with a surface. With changes in laboratory collision energy, changes in fragmentation timescale and dominant fragment ions were observed, verifying that these ions dissociate via unimolecular decay. At lower collision energies, methyl radical (CH₃) loss with a sub-microsecond dissociation rate is dominant, but consecutive H loss after CH₃ loss becomes dominant at higher collision energies. These observations are consistent with the known dissociation pathways. The dissociation rate of CH₃ loss from N(CH₃)₄⁺ formed by SPALDI and dissociated by an SID lab collision energy of 15 eV corresponds to log k = 8.1, a value achieved by laser desorption ionization (LDI) and SID at 5 eV. The results obtained with SPALDI SID and LDI SID confirm that (1) the dissociation follows unimolecular decay as predicted by RRKM calculations; (2) the SPALDI process deposits less initial energy than LDI, which has advantages for kinetics studies; and (3) fluorinated self-assembled monolayers convert about 18% of laboratory collision energy into internal energy. SID TOF experiments combined with SPALDI and peak shape analysis enable the measurement of dissociation rates for fast dissociation of small molecules.     

Analysis of Saccharides by the Addition of Amino Acids

In this work, we present the detection sensitivity improvement of electrospray ionization (ESI) mass spectrometry of neutral saccharides in a positive ion mode by the addition of various amino acids. Saccharides of a broad molecular weight range were chosen as the model compounds in the present study. Saccharides provide strong noncovalent interactions with amino acids, and the complex formation enhances the signal intensity and simplifies the mass spectra of saccharides. Polysaccharides provide a polymer-like ESI spectrum with a basic subunit difference between multiply charged chains. The protonated spectra of saccharides are not well identified because of different charge state distributions produced by the same molecules. Depending on the solvent used and other ions or molecules present in the solution, noncovalent interactions with saccharides may occur. These interactions are affected by the addition of amino acids. Amino acids with polar side groups show a strong tendency to interact with saccharides. In particular, serine shows a high tendency to interact with saccharides and significantly improves the detection sensitivity of saccharide compounds.

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Variable-temperature ion mobility time-of-flight mass spectrometry studies of electronic isomers of Kr2+ and CH3OH*+ radical cations

Preliminary results from a liquid nitrogen-cooled ion mobility (IM) orthogonal-time-of-flight (o-ToF) mass spectrometer applied to the separation of electronic isomers of Kr2+ and methanol radical cations (conventional and distonic) are presented. Ab initio calculations were used to estimate the energies and energy barriers to interconversion between conventional (CH3OH*+) and distonic (CH2*OH2+) radical cations. In addition, computations and experiments are used to compare ion-neutral collision cross-sections for CH3OH*+ and CH2*OH2+ radical cations and suggest that the mobility separation is achieved by ion-neutral interactions between ions and neutral buffer gas.     

A novel approach to collision-induced dissociation (CID) for ion mobility-mass spectrometry experiments

Collision induced dissociation (CID) combined with matrix assisted laser desorption ionization-ion mobility-mass spectrometry (MALDI-IM-MS) is described. In this approach, peptide ions are separated on the basis of mobility in a 15 cm drift cell. Following mobility separation, the ions exit the drift cell and enter a 5 cm vacuum interface with a high field region (up to 1000 V/cm) to undergo collisional activation. Ion transmission and ion kinetic energies in the interface are theoretically evaluated accounting for the pressure gradient, interface dimensions, and electric fields. Using this CID technique, we have successfully fragmented and sequenced a number of model peptide ions as well as peptide ions obtained by a tryptic digest. This instrument configuration allows for the simultaneous determination of peptide mass, peptide-ion sequence, and collision-cross section of MALDI-generated ions, providing information critical to the identification of unknown components in complex proteomic samples.     

Triboelectric spray ionization

Triboelectric spray ionization (TESI) is a variation of electrospray ionization (ESI) using common instrumental components, including gas flow, solvent flow rate and heat, the only difference being the use of a high‐voltage power supply for ESI or a static charge for TESI. The ionization of solvent or analyte is due to the electrostatic potential difference formed between the spray electrode and counter electrode. The ion source contains a pneumatic spray operated over a range of flow rates (0.15–1.5 µl/min) and gas pressures (0–100). This new design contains a standalone spray assembly and an optional metal mesh in front of the spray. There are several parameters that affect the performance during ionization of molecules including the flow rate of solvent, gas pressure, temperature, solvent acidity, distance and potential difference between emitter and counter electrode. A variable electrostatic potential can be applied for higher ionization efficiency. The new ionization method was successfully applied to solutions of various proteins under different conditions. The same charge‐state distributions compared to other ESI techniques are observed for all the protein samples. The unique feature of TESI is very efficient spraying by using a natural electrostatic potential even at the potential that a human body can produce. This provides very gentle ionization efficiency of peptides and proteins in different solvents. Copyright © 2013 John Wiley & Sons, Ltd.     

Resolution equations for high-field ion mobility

An extension of current mobility resolution equations as they apply to high-field ion mobility spectrometry is presented. The new resolution expression is applied to arrival time distributions for ions having a large range of ion mobilities and mass-to-charge ratios (m/z). The results indicate that the new equation can be utilized to predict the mobility resolution over a broader range of applied electric fields than previous ion mobility resolution expressions.     

Peak capacity of ion mobility mass spectrometry: the utility of varying drift gas polarizability for the separation of tryptic peptides

Ion mobility mass spectrometry (IM-MS) peptide mass mapping experiments were performed using a variety of drift gases (He, N2, Ar and CH4). The drift gases studied cover a range of polarizabilities ((0.2-2.6) x 10(-24) cm3) and the peak capacities obtained for tryptic peptides in each gas are compared. Although the different gases exhibit similar peak capacities (5430 (Ar) to 7580 (N2)) in some cases separation selectivity presumably based on peptide conformers (or conformer populations), is observed. For example the drift time profiles observed for some tryptic peptide ions from aldolase (rabbit muscle) show a dependence on drift gas. The transmission of high-mass ions (m/z > 2000) is also influenced by increased scattering cross-section of the more massive drift gases. Consequently the practical peak capacity for IM-MS separation cannot be assumed to be solely a function of resolution and the ability of a gas to distribute signals in two-dimensional space; rather, peak capacity estimates must account for the transmission losses experienced for peptide ions as the drift gas mass increases.