Database Search Strategies for Proteomic Data Sets Generated by Electron Capture Dissociation Mass Spectrometry

Large data sets of electron capture dissociation (ECD) mass spectra from proteomic experiments are rich in information; however, extracting that information in an optimal manner is not straightforward. Protein database search engines currently available are designed for low resolution CID data, from which Fourier transform ion cyclotron resonance (FT-ICR) ECD data differs significantly. ECD mass spectra contain both z-prime and z-dot fragment ions (and c-prime and c-dot); ECD mass spectra contain abundant peaks derived from neutral losses from charge-reduced precursor ions; FT-ICR ECD spectra are acquired with a larger precursor m/z isolation window than their low-resolution CID counterparts. Here, we consider three distinct stages of postacquisition analysis: (1) processing of ECD mass spectra prior to the database search; (2) the database search step itself and (3) postsearch processing of results. We demonstrate that each of these steps has an effect on the number of peptides identified, with the postsearch processing of results having the largest effect. We compare two commonly used search engines: Mascot and OMSSA. Using an ECD data set of modest size (3341 mass spectra) from a complex sample (mouse whole cell lysate), we demonstrate that search results can be improved from 630 identifications (19% identification success rate) to 1643 identifications (49% identification success rate). We focus in particular on improving identification rates for doubly charged precursors, which are typically low for ECD fragmentation. We compare our presearch processing algorithm with a similar algorithm recently developed for electron transfer dissociation (ETD) data

Scanning a photonic crystal slab nanocavity by condensation of xenon

Allowing xenon or nitrogen gas to condense onto a photonic crystal slab nanocavity maintained at 10–20 K results in shifts of the nanocavity mode wavelength by as much as 5 nm (~=4 meV). This occurs in spite of the fact that the mode defect is achieved by omitting three holes to form the spacer. This technique should be useful in changing the detuning between a single quantum dot transition and the nanocavity mode for cavity quantum electrodynamics experiments, such as mapping out a strong coupling anticrossing curve. Compared with temperature scanning, it has a much larger scan range and avoids phonon broadening

Steady Hall Magnetohydrodynamics Near a X-type Magnetic Neutral Line

Hall magnetohydrodynamics (MHD) properties near a two-dimensional (2D) X-type magnetic neutral line in the steady state are considered via heuristic and rigorous developments. Upon considering the steady-state as the asymptotic limit of the corresponding \textit{time-dependent} problem and using a rigorous development, Hall effects are shown to be able to sustain the hyperbolicity of the magnetic field (and hence a more open X-point configuration) near the neutral line in the steady state. The heuristic development misses this subtle connection of the steady state with the corresponding \textit{time-dependent} problem and predicts only an elongated current-sheet configuration (as in resistive MHD). However, the heuristic development turns out to be useful in providing insight into the lack of dependence of the reconnection rate on the mechanism breaking the frozen-in condition of the magnetic field lines. The latter result can be understood in terms of the ability of the ions and electrons to transport equal amounts of magnetic flux per unit time out of the reconnection region.Comment: 1-10 page

Targeted online liquid chromatography electron capture dissociation mass spectrometry for the localization of sites of in vivo phosphorylation in human Sprouty2

We demonstrate a strategy employing collision-induced dissociation for phosphopeptide discovery, followed by targeted electron capture dissociation (ECD) for site localization. The high mass accuracy and low background noise of the ECD mass spectra allow facile sequencing of coeluting isobaric phosphopeptides, with up to two isobaric phosphopeptides sequenced from a single mass spectrum. In contrast to the previously described neutral loss of dependent ECD method, targeted ECD allows analysis of both phosphotyrosine peptides and lower abundance phosphopeptides. The approach was applied to phosphorylation analysis of human Sprouty2, a regulator of receptor tyrosine kinase signaling. Fifteen sites of phosphorylation were identified, 11 of which are novel

The apparatus composition and architecture of Erismodus quadridactylus and the implications for element homology in prioniodinin conodonts

The apparatus composition and architecture of prioniodinin conodonts is poorly understood, largely because few prioniodinin taxa are represented by articulated oral feeding apparatuses (natural assemblages) in the fossil record, but also due to the highly variable gradational morphology of their constituent elements that makes apparatus reconstruction problematic. We describe here a natural assemblage of Erismodus quadridactylus (Stauffer), a prioniodinin, from the Sandbian (Late Ordovician) of North Dakota, USA. The assemblage demonstrates that the apparatus architecture of Erismodus is similar to those of late Palaeozoic prioniodinins namely, Kladognathus Rexroad and Hibbardella Bassler, but also has similarities with ozarkodinin apparatuses. In addition, there is evidence to suggest that E. quadridactylus shares topological similarities to balognathid architecture, with respect to the position of its inferred P elements. The apparatus composition and architecture presented here indicate that, at least with respect to the M–S array, an ‘ozarkodinin‐type’ bauplan is probably more widely representative across prioniodontids. The assemblage demonstrates that element morphotypes traditionally considered to lie within the S array are M elements, whereas others traditionally interpreted as P elements are found in the S array. These observations are used as a basis for refining concepts of element homology among prioniodinin conodonts and their closest relatives

Psychotic Alzheimer\u27s disease is associated with gender-specific tau phosphorylation abnormalities

Converging evidence suggests that psychotic Alzheimer\u27s disease (AD + P) is associated with an acceleration of frontal degeneration, with tau pathology playing a primary role. Previous histopathologic and biomarker studies have specifically implicated tau pathology in this condition. To precisely quantify tau abnormalities in the frontal cortex in AD + P, we used a sensitive biochemical assay of total tau and 4 epitopes of phospho-tau relevant in AD pathology in a postmortem sample of AD + P and AD - P. Samples of superior frontal gyrus from 26 AD subjects without psychosis and 45 AD + P subjects with psychosis were analyzed. Results of enzyme-linked immunosorbent assay demonstrate that AD + P females, but not males, had significantly higher levels of phosphorylated tau in the frontal cortex. In males, but not females, AD + P was associated with the presence of alpha-synuclein pathology. These results support a gender dissociation of pathology in AD + P. The design of future studies aimed at the elucidation of cognitive and/or functional outcomes; regional brain metabolic deficits; or genetic correlates of AD + P should take gender into consideration. (C) 2014 Elsevier Inc. All rights reserved

Quantum dot photonic crystal nanocavities: Transition from weak to strong coupling and nonlinear emissions

Photonic crystal slab nanocavities containing one layer of quantum dots have exhibited: strong coupling to a single quantum dot; tuning by condensation of xenon gas; linewidth broadening due to ensemble dot absorption; gain and lasing

The Economic Resource Receipt of New Mothers

U.S. federal policies do not provide a universal social safety net of economic support for women during pregnancy or the immediate postpartum period but assume that employment and/or marriage will protect families from poverty. Yet even mothers with considerable human and marital capital may experience disruptions in employment, earnings, and family socioeconomic status postbirth. We use the National Survey of Families and Households to examine the economic resources that mothers with children ages 2 and younger receive postbirth, including employment, spouses, extended family and social network support, and public assistance. Results show that many new mothers receive resources postbirth. Marriage or postbirth employment does not protect new mothers and their families from poverty, but education, race, and the receipt of economic supports from social networks do