IMSPeptider: A computational peptide collision cross‐section area calculator based on a novel molecular dynamics simulation protocol

Introduction of ion mobility mass spectrometry (IMS/MS) into the proteomic workflow provides an orthogonal separation to the widely used LC‐MS platforms. IMS also provides structural information that could facilitate peptide identification. However, the lack of tools capable of predictive power in a high‐throughput fashion makes peptide global profiling quite challenging. To target this issue, a computational workflow was developed based on biophysical principles to predict the collision cross‐section area (CCS) of peptides as measured from IMS/MS experiments. Hosted on a web server, it allows the user to input a primary sequence (query) and retrieve information on peptide structure, sequence, and corresponding CCS. The current version is designed to identify peptide sequences up to 23 residues in length, in its higher charge state, based on a match of the molecule m/z and CCS. The protocol was validated against a 128‐sequences‐dataset and CCS predicted within 2.8% average error. © 2013 Wiley Periodicals, Inc.     

The Infrared Spectrum of Crystalline Methyl Formate

Abstract

The vibrational spectra of methyl formate have been recorded and analyzed by many workers^1. As a result, the vibrational assignment and molecular conformation is well known. None of these workers have reported the infrared spectra of crystalline methyl formate, however, and only one group¹ has reported the Raman spectrum of the crystalline compound. In addition, there appears to be no report in the literature concerning the crystal structure of methyl formate by diffraction or other methods. This is perhaps not surprising in view of the compounds low melting point (?99°C). Since methyl formate is the first and simplest member of the ester class, it seemed desirable to have some data on the infrared spectra of the crystal even though the detailed analysis of such data, in the absence of a reported cyrstal structure, is difficult and uncertain. Nevertheless, it is often possible to draw some conclusions concerning the nature of the crystalline material, particularly if an oriented sample can be obtained so tha polarized radiation can be used.     

Facile design of degradable poly(β‐thioester)s with tunable structure and functionality

The synthesis of a range of linear biodegradable poly(β‐thioester)s, PBTs, via hexylamine‐catalyzed thiol‐ene Micheal additions between a variety of diacrylate and dithiol monomers is described. Molecular weights up to 12,000 g mol^?1 are obtained for this new class of polymer materials. PBTs featuring very different chemical and mechanical behavior are obtained on the basis of seven diacrylate and three dithiol monomers. Polar PBTs are synthesized based on ethylene glycol‐containing monomers in an environmentally friendly solvent. Furthermore, PBTs containing urethane units in the main chain are obtained, providing access to an isocyanate‐free polyurethane polymerization method. The thiol‐ene addition approach can also be used to couple polystyrene oligomers synthesized from a bifunctional trithiocarbonate reversible addition fragmentation transfer agent. In this way, PBTs featuring polystyrene segments as well as diacrylate segments are produced. In general for these step‐growth polymerizations, by tuning the stoichiometric monomer ratio, a desired end group functionality can be quantitatively introduced into the PBT, which is demonstrated via soft ionization mass spectrometry analysis. As an example, alkyne end groups have been built in, giving access to use these materials in modular polymer design strategies. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 178–187     

A characterization of discrete groups

The purpose of this article is to prove the following result. Let be a locally compact group, the Fourier algebra of and ~0$"> such that . Then is a discrete group .

     

Analysis of succinylacetone, as a Girard T derivative, in urine and dried bloodspots by flow injection electrospray ionization tandem mass spectrometry

Flow injection electrospray ionization tandem mass spectrometric methods for succinylacetone (SA) in 250 microL urine, using d5-SA as internal standard, and in 3 mm dried bloodspots, using 13C4-SA as internal standard, are described. Selectivity and sensitivity of analysis is achieved by the use of a mono-Girard T derivative. Measured SA infant urine normal range (n=20) is 0.013-0.27 micromol/mmol creatinine. Measured SA newborn bloodspot normal range (n=152) is 0-0.30 micromol/L. Bloodspots from children with hepatorenal tyrosinemia type 1, and kept at room temperature for up to 7 years, afforded SA concentrations of 0.9-5.7 micromol/L.     

Malolactonate polymers and copolymers for biomedical applications

A new class of malolactonate polymers and copolymers with a wide range of lateral chain structures were synthesized by anionic ring opening polymerization of alkyl malolactonate monomers. The monomers were prepared in good yields according to established procedures. Final macromolecular and thermal characteristics were in agreement with the designed monomer structures. Molecular weights in the range 4-20 kD were attained, as a result of chain transfer reactions. Representative polymeric compounds displayed stability up to 200 °C. Many of the obtained poly(alkyl malolactonate)s were able to sustain and promote with 3T3 murine fibroblasts adhesion and proliferation onto their surface.     

Evidence of formation of ammonium perfluorononanoate/2H2O multilamellar vesicles: morphological analysis by rheology and rheo-2H NMR experiments

Rheology and rheo-(2)H NMR measurements are presented for 30 wt % ammonium perfluorononanoate (APFN)/(2)H(2)O mixture in the temperature range 20-70 °C. A first-order lamellar-to-nematic transition occurs at 42 °C, and a first-order nematic-to-isotropic transition occurs at 49 °C. Different rheological behaviors of the lamellar phase were observed with increasing the temperature. The lamellar structure at low temperature (Lα(-)) has a clear gel-like viscoelasticity, while at high temperature the lamellar structure (Lα(+)) has a liquid-like response. In this study we have observed for the first time, along with the lamellar phase of a surfactant containing fluorinated fatty acid, the formation of multilamellar vesicles (MLVs) ("onions") induced by shear. With the aid of nonlinear rheology and rheo-NMR techniques, onion formation was found to occur in both temperature regimes of the lamellar phase, but at different strain units. It is suggested that the lamellar phase consists of smectic structures in both Lα(-) and Lα(+), but with different percentages of defect density.     

Intracellular pH measurements made simple by fluorescent protein probes and the phasor approach to fluorescence lifetime imaging

A versatile pH-dependent fluorescent protein was applied to intracellular pH measurements by means of the phasor approach to fluorescence lifetime imaging. By this fit-less method we obtain intracellular pH maps under resting or altered physiological conditions by single-photon confocal or two-photon microscopy.     

Two dimensional patterning of fluorescent proteins in hydrogels

This work describes the successful micropatterning of hybrid systems consisting of hydrogel-dispersed optically active and controllable proteins on solid surfaces without degradation of the photophysical properties of the light-emitting biomolecules. It demonstrates the preservation of the luminescence properties of proteins entrapped into isolated microstructures of poly(acrylamide) gel. This way we can exploit both the structural and function-preserving properties of the hydrogels and the functionality of light-emitting proteins. We believe that this approach can open the way to the realization of nanopatterned optical memories based on photochromic biomolecules.