SILVER helps assign peptides to tandem mass spectra using intensity-based scoring

Tandem mass spectrometry is commonly used to identify peptides (and thereby proteins) that are present in complex mixtures. Peptide identification from tandem mass spectra is partially automated, but still requires human curation to resolve "borderline" peptide-spectrum matches (PSMs). SILVER is web-based software that assists manual curation of tandem mass spectra, using a recently developed intensity-based machine-learning approach to scoring PSMs, Elias et al. In this method, a large training set of peptide, fragment, and peak-intensity properties for both matched and mismatched PSMs was used to develop a score measuring consistency between each predicted fragment ion of a candidate peptide and its corresponding observed spectral peak intensity. The SILVER interface provides a visual representation of match quality between each candidate fragment ion and the observed spectrum, thereby expediting manual curation of tandem mass spectra. SILVER is available online at http://llama.med.harvard.edu/Software.html.     

Development of a fluorescence lifetime-based sol-gel humidity sensor

A sol-gel-based optical sensor for the measurement of relative humidity has been developed. It is based on the changes in fluorescence intensity and/or lifetime of the ruthenium complex, ruthenium(II)diphenylphenanthroline-dipyridophenazinehexafluorophosphate. Sensitivity to relative humidity has been demonstrated over the range 0-100% relative humidity. This sensor has been developed for application in the field of indoor air-quality monitoring and displays a limit of detection of 0.35% relative humidity and a resolution of 1.13% over the concentration range of interest (0-50% relative humidity). The effects of varying process parameters on the sensor performance were studied along with the effects of cross-sensitivity to molecular oxygen.     

Hydride abstraction in fast atom bombardment

Under fast atom bombardment conditions, compounds having long alkyl chains may exhibit [M ? H]⁺ as the major quasimolecular ion species, which can lead to incorrect assignment of molecular masses. It is shown that for a long-chain ether the loss of the hydride occurs from the hydrocarbon chain remote from the oxygen. This effect may yield information concerning ionization mechanisms in fast atom bombardment/mass spectrometry.     

Kohn’s theorem, Larmor’s equivalence principle and the Newton–Hooke group

We consider non-relativistic electrons, each of the same charge to mass ratio, moving in an external magnetic field with an interaction potential depending only on the mutual separations, possibly confined by a harmonic trapping potential. We show that the system admits a “relativity group” which is a one-parameter family of deformations of the standard Galilei group to the Newton–Hooke group which is a Wigner–?nönü contraction of the de Sitter group. This allows a group-theoretic interpretation of Kohn’s theorem and related results. Larmor’s theorem is used to show that the one-parameter family of deformations are all isomorphic. We study the “Eisenhart” or “lightlike” lift of the system, exhibiting it as a pp-wave. In the planar case, the Eisenhart lift is the Brdi?ka–Eardley–Nappi–Witten pp-wave solution of Einstein–Maxwell theory, which may also be regarded as a bi-invariant metric on the Cangemi–Jackiw group.     

Purely nonlocal Hamiltonian formalism for systems of hydrodynamic type

We study purely nonlocal Hamiltonian structures for systems of hydrodynamic type. In the case of a semi-Hamiltonian system, we show that such structures are related to quadratic expansions of the diagonal metrics naturally associated with the system.     

Animal network phenomena: Insights from triadic games

Triadic interactions have a very important role to play in games of animal conflict on complex networks, because triads are both the simplest groups in which asymmetric network phenomena can be studied and the groups beyond dyads in which analysis of population games is most likely to be tractable, especially when allowing for intrinsic variation. Here we demonstrate how analytical models of triadic games can yield novel insights into a variety of behavioral phenomena within networks, including coalition formation, eavesdropping, and victory displays. © 2008 Wiley Periodicals, Inc. Complexity, 2009     

A qualitative study of amlodipine and its related compounds by electrospray ionization tandem mass spectrometry

A comprehensive structural analysis of amlodipine and certain related compounds was performed by electrospray ionization tandem mass spectrometry. Triple quadrupole and quadrupole time-of-flight instruments were used to provide collision-induced dissociation and accurate mass measurement for selected product and second-generation product ions. A unique ion rearrangement was observed, which was found to be characteristic of certain dihydropyridines. This study provides a fundamental understanding of the fragmentation of these compounds. The structural elucidation of an unknown impurity is presented as an example.