A physical model of axonal damage due to oxidative stress.

Oxidative damage is implicated in the pathogenesis of neurodegenerative disorders, including Alzheimer's, Parkinson's, and Huntington's diseases, and in normal aging. Here, we model oxidative stress in neurons using photogenerated radicals in a simplified membrane-encapsulated microtubule system. Using fluorescence and differential interference contrast microscopies, we monitor photochemically induced microtubule breakdown on the supported region of membrane in encapsulating synthetic liposomes as a function of lipid composition and environment.

Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers.

The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm.

Cis-trans signatures of proline-containing tryptic peptides in the gas phase.

High-resolution ion mobility/time-of-flight techniques were used to measure collision cross sections for 968 tryptic digest peptide ions obtained from digestion of common proteins. Here, we report a mobility signature that aids in identifying proline-containing peptides containing 4-10 residues. Of 129 peptides (< or = 10 residues in length) in the database that contain proline residues, 57% show multiple resolved features in the ion mobility distribution for at least one of the [M + H]+ or [M + 2H]2+ ions.

Coupling ion mobility separations, collisional activation techniques, and multiple stages of MS for analysis of complex peptide mixtures.

An ion trap/ion mobility/quadrupole/collision cell/time-of-flight mass spectrometer that incorporates a differentially pumped orifice-skimmer cone region at the back of the drift tube has been developed for the analysis of peptide mixtures. The combined approach allows a variety of strategies to be employed for collisionally activating ions, and fragments can be monitored by subsequent stages of mass spectrometry in a parallel fashion, as described previously (Anal. Chem.

Prediction of peptide ion collision cross sections from topological molecular structure and amino acid parameters.

Quantitative structure-property relationships (QSPRs) have been developed to predict the ion mobility spectrometry (IMS) collision cross sections of singly protonated lysine-terminated peptides using information derived from topological molecular structure and various amino acid parameters. The primary amino acid sequence alone is sufficient to accurately predict the collision cross section. The models were built using multiple linear regression (MLR) and computational neural networks (CNNs).