Collidoscope: An Improved Tool for Computing Collisional Cross Sections with the Trajectory Method

Ion Mobility-Mass Spectrometry (IM-MS) can be a powerful tool for determining structural information about ions in the gas phase, from small covalent analytes to large, unfolded, and/or denatured proteins and complexes. For large biomolecular ions, which may have a wide variety of possible gas-phase conformations and multiple charge sites, quantitative, physically explicit modeling of collisional cross sections (CCSs) for comparison to IMS data can be challenging and time-consuming. We present a “trajectory method” (TM) based CCS calculator, named “Collidoscope”, which utilizes parallel processing and optimized trajectory sampling, and implements both He and N2 as collision gas options. Also included is a charge-placement algorithm for determining probable charge site configurations for protonated protein ions given an input geometry in pdb file format. Results from Collidoscope are compared to those from the current state-of-the-art CCS simulation suite, IMoS. Collidoscope CCSs are typically within 4% of IMoS values for ions with masses from ~18 Da to ~800 kDa. Collidoscope CCSs using x-ray crystal geometries are typically within a few percent of IM-MS experimental values for ions with mass up to ~3.5 kDa (melittin), and discrepancies for larger ions up to ~800 kDa (GroEL) are attributed in large part to changes in ion structure during and after the electrospray process. Due to its physically explicit modeling of scattering, computational efficiency, and accuracy, Collidoscope can be a valuable tool for IM-MS research, especially for large biomolecular ions

Extended Protein Ions are Formed by the Chain Ejection Model in Chemical Supercharging Electrospray Ionization

Supercharging electrospray ionization can be a powerful tool for increasing charge states in mass spectra and generating unfolded ion structures, yet key details of its mechanism remain unclear. The structures of highly extended protein ions and the mechanism of supercharging were investigated using ion mobility-mass spectrometry. Head-to-tail-linked polyubiquitins (Ubq1−11) were used to determine size and charge state scaling laws for unfolded protein ions formed by supercharging while eliminating amino acid composition as a potential confounding factor. Collisional cross section was found to scale linearly with mass for these ions and several other monomeric proteins, and the maximum observed charge state for each analyte scales with mass in agreement with an analytical charge state scaling law for protein ions with highly extended structures that is supported by experimental gas-phase basicities. These results indicate that these highly unfolded ions can be considered quasi-one-dimensional, and collisional cross sections modeled with the Trajectory Method in Collidoscope show that these ions are significantly more extended than linear α-helices but less extended than straight chains. The effect of internal disulfide bonds on the extent of supercharging was probed using bovine serum albumin, β-lactoglobulin, and lysozyme, each of which contains multiple internal disulfide bonds. Reduction of the disulfide bonds led to a marked increase in charge state upon supercharging without significantly altering folding in solution. This evidence supports a supercharging mechanism in which these proteins unfold before or during evaporation of the electrospray droplet and ionization occurs by the Chain Ejection Model

Can Food Stamps Do More to Improve Food Choices? An Economic Perspective

Food stamp recipients, like other Americans, struggle with nutrition problems associated with choice of foods, as well as amounts. This series of Economic Information Bulletins compiles evidence to help answer the question of whether the Food Stamp Program can do more to improve the food choices of participants. It examines the role of affordability and price of healthful foods in influencing food choices and the likely success of any policy targeted at changing food choices through food stamp bonuses or restrictions. It also examines other approaches to changing food choices, including nutrition education and potential strategies drawn from behavioral economics literature. Meaningful improvements in the diets of food stamp recipients will likely depend on a combination of many tactics. Measuring the effect of any policy change on food choices and health outcomes remains a challenge.Food Stamp Program, food consumption, food prices, food expenditures, nutrition education, behavioral economics, food choices, diet, health, fruits and vegetables, Food Assistance and Nutrition Research Program, FANRP, ERS, USDA, Agricultural and Food Policy, Consumer/Household Economics, Food Consumption/Nutrition/Food Safety, Institutional and Behavioral Economics,

Averages of b-hadron Properties at the End of 2005

This article reports world averages for measurements on b-hadron properties obtained by the Heavy Flavor Averaging Group (HFAG) using the available results as of at the end of 2005. In the averaging, the input parameters used in the various analyses are adjusted (rescaled) to common values, and all known correlations are taken into account. The averages include lifetimes, neutral meson mixing parameters, parameters of semileptonic decays, branching fractions of B meson decays to final states with open charm, charmonium and no charm, and measurements related to CP asymmetries

Protonation Isomers of Highly Charged Protein Ions Can Be Separated in FAIMS-MS

High-field asymmetric waveform ion mobility spectrometry-mass spectrometry (FAIMS-MS) can resolve over an order of magnitude more conformers for a given protein ion than alternative methods. Such an expansion in separation space results, in part, from protein ions with masses of \u3e29 kDa undergoing dipole alignment in the high electric field of FAIMS, and the resolution of ions that adopt pendular vs free rotor states. In this study, FAIMS-MS, collision-induced dissociation (CID), and travelling wave (TW) IMS-MS were used to investigate the pendular and free rotor states of protonated carbonic anhydrase II (CAII, 29 kDa). The electrospray ionization additive 1,2-butylene carbonate was used to increase protein charge states and ensure extended ion conformations were formed. For relatively high charge states in which dipole alignment occurs (30e38þ), FAIMS-MS can baseline resolve the isobaric pendular and free rotor ion populations. For TWIMS-MS, these same charge states resulted in monomodal arrival time distributions with collision cross sections corresponding to highly extended ion conformations. Interestingly, CID of FAIMS-selected pendular and free rotor ion populations resulted in significantly different frag-mentation patterns. For example, CID of the dipole aligned CAII 37þ resulted in cleavages C-terminal to residue 183, 192 and 196, whereas cleavage sites for the free rotor population occurred near residues 12 and 238. Given that the cleavage sites are ’directed’ by protonation sites in the CID of protein ions, and highly charged protein ions adopt extended conformations with the same or very similar collision cross sections, these results indicate that the pendular and free rotor populations separated in FAIMS can be attributed to protonation isomers. Moreover, the extent of protein ion charging in FAIMS-MS decreased substantially as the carrier gas flow rate decreased, indicating that ion charging in FAIMS-MS can be limited by proton-transfer reactions. Given that the total mass of proton charge carriers corresponds to less than 0.2% the mass of CAII, we anticipate that FAIMS-MS can be used to separate intact isobaric proteoforms with masses of at least ~29 kDa that result from alternative sites of post-translational modifications

Study of 3-prong Hadronic τ\tau Decays with Charged Kaons

Using a sample of 4.7/fb integrated luminosity accumulated with the CLEO-II detector at the Cornell Electron Storage Ring (CESR), we have measured the branching fractions of the tau lepton into $K^- h^+ \pi^- \nu_\tau$ and $K^- K^+ \pi^- \nu_\tau$ relative to $h^- h^+ h^- \nu_\tau; K^- h^+ \pi^- \pi^0\nu_\tau$ and $K^- K^+ \pi^- \pi^0\nu_\tau$ relative to $h^- h^+ h^- \pi^0 \nu_\tau$. The relative branching fractions are: (5.16+-0.20+-0.50)*$10^{-2}$, (1.52+-0.14+-0.29)*$10^{-2}$, (2.54+-0.44+-0.39)*$10^{-2}$ and $<0.0154$ at 95% C.L., respectively. Coupled with additional experimental information, we use our results to extract information on the structure of three-prong tau decays to charged kaons.Comment: 16 pages postscript file also available through http://w4.lns.cornell.edu/public/CLN

The Atlantic Ocean at the last glacial maximum: 1. Objective mapping of the GLAMAP sea-surface conditions

Recent efforts of the German paleoceanographic community have resulted in a unique data set of reconstructed sea-surface temperature for the Atlantic Ocean during the Last Glacial Maximum, plus estimates for the extents of glacial sea ice. Unlike prior attempts, the contributing research groups based their data on a common definition of the Last Glacial Maximum chronozone and used the same modern reference data for calibrating the different transfer techniques. Furthermore, the number of processed sediment cores was vastly increased. Thus the new data is a significant advance not only with respect to quality, but also to quantity. We integrate these new data and provide monthly data sets of global sea-surface temperature and ice cover, objectively interpolated onto a regular 1°x1° grid, suitable for forcing or validating numerical ocean and atmosphere models. This set is compared to an existing subjective interpolation of the same base data, in part by employing an ocean circulation model. For the latter purpose, we reconstruct sea surface salinity from the new temperature data and the available oxygen isotope measurements

First Observation of Υ(1S)→γππ\Upsilon(1S)\to \gamma\pi\pi

We report on a study of exclusive radiative decays of the Upsilon(1S) resonance collected with the CLEO-II detector operating at CESR. We present the first observation of the radiative decays Upsilon(1S)->gamma pi+pi- and Upsilon(1S)->gamma pi0pi0. For the dipion mass regime m(pipi)>1.0 GeV, we obtain Br(Upsilon(1S)->gamma pi+pi-=(6.3+/-1.2+/-1.3) x 10^(-5), and Br(Upsilon(1S)->gamma pi0pi0=(1.7+/-0.6+/-0.3) x 10^(-5). The observed gamma pipi events are consistent with the hypothesis Upsilon(1S)->gamma f2(1270).Comment: 9 pages, postscript file also available through http://w4.lns.cornell.edu/public/CLN

Search for a Scalar Bottom Quark with Mass 3.5-4.5 GeV/c2c^{2}

We report on a search for a supersymmetric $\tilde{B}$ meson with mass between 3.5 and 4.5 GeV/$c^2$ using 4.52 ${\rm fb}^{-1}$ of integrated luminosity produced at $\sqrt{s}=10.52$ GeV, just below the $e^+e^-\to B\bar{B}$ threshold, and collected with the CLEO detector. We find no evidence for a light scalar bottom quark.Comment: 10 pages postscript, also available through http://w4.lns.cornell.edu/public/CLN