Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution

Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting “pure” IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810–1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) “shift factors” to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.₈ Å², 295.₁ Å², 296.₈ Å², and 300.₁ Å²; all four of these CCS values were within 1.5% of independently measured DTIM-MS values.     

A collision cross-section database of singly-charged peptide ions

A database of ion-neutral collision cross-sections for singly-charged peptide ions is presented. The peptides included in the database were generated by enzymatic digestion of known proteins using three different enzymes, resulting in peptides that differ in terms of amino acid composition as well as N-terminal and C-terminal residues. The ion-neutral collision cross-sections were measured using ion mobility (IM) spectrometry that is directly coupled to a time-of-flight (TOF) mass spectrometer. The ions were formed by a matrix-assisted laser desorption ionization (MALDI) ion source operated at pressures (He bath gas) of 2 to 3 torr. The majority (63%) of the peptide ion collision cross-sections correlate well with structures that are best described as charge-solvated globules, but a significant number of the peptide ions exhibit collision cross-sections that are significantly larger or smaller than the average, globular mobility-mass correlation. Of the peptide ions having larger than average collision cross-sections, approximately 71% are derived from trypsin digestion (C-terminal Arg or Lys residues) and most of the peptide ions that have smaller (than globular) collision cross-sections are derived from pepsin digestion (90%).     

Profiling and imaging of tissues by imaging ion mobility-mass spectrometry

Molecular profiling and imaging mass spectrometry (IMS) of tissues can often result in complex spectra that are difficult to interpret without additional information about specific signals. This report describes increasing data dimensionality in IMS by combining two-dimensional separations at each spatial location on the basis of imaging ion mobility-mass spectrometry (IM-MS). Analyte ions are separated on the basis of both ion-neutral collision cross section and m/z, which provides rapid separation of isobaric, but structurally distinct ions. The advantages of imaging using ion mobility prior to MS analysis are demonstrated for profiling of human glioma and selective lipid imaging from rat brain.     

Axiomatizations of the Euclidean compromise solution

A multicriteria optimization problem is one of choosing an alternative that optimizes several—possibly conflicting—objective functions simultaneously. The utopia point of a multicriteria optimization problem is the vector that specifies for each objective function the most favorable feasible value. The Euclidean compromise solution in multicriteria optimization is a solution that selects from a feasible set the alternative such that its vector of criteria values has minimal Euclidean distance to the utopia point. This paper provides several axiomatic characterizations of the Euclidean compromise solution that are based on consistency properties.     

Application of Fragment Screening and Merging to the Discovery of Inhibitors of the Mycobacterium tuberculosis Cytochrome P450 CYP121

Pieces of the puzzle: The first fragment-based approach was used to target cytochrome?P450 enzymes (CYPs) for drug development. The experiments provide new insights into the binding site of the essential Mycobacterium tuberculosis CYP121 enzyme, and resulted in a promising novel lead compound based on fragment merging.     

Raman spectroscopy of dipyrrins: nonresonant,resonant and surface‐enhanced cross‐sections and enhancement factors

Detailed studies of the mechanism of surface‐enhanced (resonance) Raman spectroscopy (SE(R)RS), and its applications, place a number of demands on the properties of SERS scatterers. With large Raman cross‐sections, versatile synthetic chemistry and complete lack of fluorescence, free dipyrrins meet these demands but the Raman and SE(R)RS spectroscopy of free dipyrrins is largely unknown. The first study of the Raman spectroscopy of free dipyrrins is therefore presented in this work. The nonresonant Raman, resonant Raman and surface‐enhanced Raman spectra of a typical meso aryl‐substituted‐dipyrrin are reported. Absolute differential cross‐sections are obtained for excitation wavelengths in the near infrared and visible region, in solution phase and for dipyrrin adsorbed on the surface of silver nanoparticles. Raman enhancement factors for SERRS and resonance Raman are calculated from the observed differential cross‐sections. The magnitudes of the resonantly enhanced cross‐sections are similar to those recently reported for strong SERS dyes such as Rhodamine 6G and Crystal Violet. Free dipyrrins offer the advantages of existing SERS dyes but without the drawback of strong fluorescence. Free dipyrrins should therefore find applications in all areas of Raman spectroscopy including fundamental studies of the mechanisms of SERS and bioanalytical and environmental applications. Copyright © 2011 John Wiley & Sons, Ltd.     

Microscale Fracture Toughness of Bismuth Doped Copper Bicrystals Using Double Edge Notched Microtensile Tests

The availability of focused ion beam (FIB) milling, nanoindentation, and microelectromechanical systems (MEMS) based test platforms has enabled small-scale mechanical testing to become an increasingly popular approach for measuring material properties. While great emphasis has been placed on measuring plastic properties at the micro- and nanoscale [1, 2], an area that has received significantly less consideration is the measurement of fracture toughness. A technique for performing small-scale, in situ fracture toughness tests using double edge notched tensile (DENT) specimens has been developed and used to measure a nearly 40 % reduction in toughness associated with the addition of Bi to the grain boundary of a Cu bicrystal. That Bi embrittles Cu grain boundaries is well known [3–10], however, as shown herein, the DENT technique offers certain advantages over existing boundary fracture tests, especially when used with ductile materials.     

A two-sided Arnoldi algorithm with stopping criterion and MIMO selection procedure

In this paper we introduce a two-sided Arnoldi method for the reduction of high order linear systems and we propose useful extensions, first of all a stopping criterion to find a suitable order for the reduced model and secondly, a selection procedure to significantly improve the performance in the multi-input multi-output (MIMO) case. One application is in micro-electro-mechanical systems (MEMS). We consider a thermo-electric micro thruster model, and a comparison between the commonly used Arnoldi algorithm and the two-sided Arnoldi is performed.     

Diagnosing laser-driven,shock-heated foam target with Al absorption spectroscopy on OMEGA EP

Results on diagnoses of laser-driven, shock-heated foam plasma with time-resolved Al 1s-2p absorption spectroscopy are reported. Experiments were carried out to produce a platform for the study of relativistic electron transport. In cone-guided Fast Ignition (FI), relativistic electrons generated by a high-intensity, short-pulse igniter beam must be transported through a cone tip to an imploded core. Transport of the energetic electrons could be significantly affected by the temperature-dependent resistivity of background plasmas. The experiment was conducted using four UV beams of the OMEGA EP laser at the Laboratory For Laser Energetics. One UV beam (1.2 kJ, 3.5 ns square) was used to launch a shock wave into a foam package target, consisting of 200 mg/cm³ CH foam with aluminum dopant and a solid plastic container surrounding the foam layer. The other three UV beams with the total energy of 3.2 kJ in 2.5 ns pulse duration were tightly focused onto a Sm dot target to produce a point X-ray source in the energy range of 1.4–1.6 keV. The quasi-continuous X ray signal was transmitted through the shock-heated Al-doped, foam layer and recorded with an X-ray streak camera. The measured 1s-2p Al absorption features were analyzed using an atomic physics code FLYCHK. Electron temperature of 40 eV inferred from the spectral analysis is consistent with 2-D DRACO Radiation-hydrodynamic simulations.