i-RUBY: a novel software for quantitative analysis of highly accurate shotgun-proteomics liquid chromatography/tandem mass spectrometry data obtained without stable-isotope labeling of proteins

We developed a novel software named i-RUBY (identification-Related qUantification-Based strategY algorithm for liquid chromatography/tandem mass spectrometry (LC/MS/MS) data) that enables us to perform fully automatic ion current-based spectral feature analysis of highly accurate data obtained by LC/MS/MS. At the 1st step, this software utilizes accurate peptide/protein identification information for peak detection and peak matching among measurements. Then, at the 2nd step, it picks yet unidentified peaks and matches them to the peaks identified at the 1st step by a linear interpolation algorithm. The analysis of human plasma externally spiked with a known amount of yeast alcohol dehydrogenase 1 showed a good linear relationship between the amount of protein spiked and the quantitative values obtained by i-RUBY analysis. Experiment using human plasma digests spiked with a mixture of known amounts of synthetic peptides derived from two yeast proteins, alcohol dehydrogenase 1 and glucose-6-phospate isomerase, showed the expansion by the 2nd step of i-RUBY of the lower quantification limits to 1/10 to 1/1000 of those reached only by identified peaks at the 1st step. Good correlations between the i-RUBY results and the amount of proteins were confirmed by the analysis of real samples, i.e., sera of normal subjects and cancer patients, by comparing quantitative values of acute-phase proteins obtained by i-RUBY analysis of LC/MS/MS data with those obtained by an immunological method using Bio-Plex. These results taken together show that i-RUBY is a useful tool for obtaining dependable quantitative information from highly accurate shotgun-proteomics LC/MS/MS data.     

ALMA Band 10 tertiary optics

The ALMA Band 10 (787–950 GHz) receiver is a dual-polarization heterodyne system based on NbTiN superconducting technology. The coupling of energy from the secondary mirror of the ALMA Cassegrain antenna to the Superconductor–Insulator–Superconductor (SIS) mixers used for down-conversion is achieved by a frequency-independent optical system composed of two elliptical mirrors to focus and redirect the incoming radiation, a wire-grid to separate orthogonal linear polarizations and two corrugated horns, one for each polarization and SIS mixer. In this paper, we present the ALMA Band 10 tertiary optics design and evaluate its performance by quasi-optical techniques, Physical Optics simulations and measurements. Detailed results of secondary aperture efficiency and beam-squint are provided. The characterization procedure described in this paper can be used for any optical system at around 1 THz.     

Preparation and characterization of fiber-textured SrAl2O4:Eu films grown using a homo-buffer layer

This paper describes the preparation and characterization of fiber-textured SrAl₂O₄:Eu films on a quartz glass substrate using a homo-buffer layer. The effect of the buffer layer on the crystallinity and adhesion was investigated by cross-section transmission electron microscopy and X-ray diffraction (XRD). The results show that the prepared film was not only well crystallized but also highly textured. The preferred orientation of this textured film was confirmed to be (0 3 1) by pole figure measurement. In addition, this film exhibits excellent optical transparency, with an average transmittance of more than 80% in the visible range.     

Application of a Stopped-Flow EPR Method for the Detection of Short-Lived Flavonoid Semiquinone Radicals Produced by Oxidation Using <Superscript>15</Superscript>N-Labeled Nitrosodisulfonate Radical (Fremy’s Salt)

A stopped-flow-electron paramagnetic resonance (EPR) method was applied for the detection of short-lived radicals of flavonoids bearing a catechol moiety as the B-ring, such as flavonols (quercetin, fisetin, and rutin), flavanones (eriodictyol and taxifolin), flavanols (catechin and epicatechin), and flavone (luteolin). ¹⁵N-labeled sodium salt of nitrosodisulfonate (¹⁵NDS) was employed to obtain the highly resolved EPR hyperfine structure (hfs) of flavonoid-derived semiquinone radicals under stoichiometrically regulated reaction conditions in aqueous media (pH 10). The EPR hfs of these flavonoids radicals, except catechin and epicatechin, were recorded. Based on the g value and the proton hyperfine coupling constants (hfcc), these flavonoid-derived radicals were assigned to be semiquinone radicals of the catechol moiety (B-ring). For example, the observed EPR hyperfine structure (hfs) of the luteolin radical (Lut^?·) was composed of four sets of doublet splitting, which could be ascribed to the three protons of the B-ring (a^2′?=?0.136, a^5′?=?0.102, and a^6′?=?0.272 mT) and a vinyl proton of the C-ring (a³?=?0.099 mT). In addition, the characteristically small doublet splitting resolved for the fisetin anion radical (Fis^?·, 0.028 mT) was assigned to the aromatic proton at the C₅ carbon of the A-ring, indicating that the unpaired electron of the radials was partially delocalized onto the A-ring through the π bonds involved in the vinyl-carbonyl moiety of the C-ring. The hfcc of the methine protons at the C₂ carbon of taxifolin and eriodictyol-derived radicals (Tax^?· and Eri^?·) was, respectively, evaluated to be 0.102 and 0.230 mT. The assignment of the proton hfcc of flavonoid-derived semiquinone radicals will be discussed in relation with the molecular structure of the C-ring.     

Polarized light-induced anisotropy depending on polymer matrices studied by polarized ftir spectroscopy

Polarized-light induced anisotropy of Disperse Orange 3 (DO3) depending on the polymer matrices was investigated by polarized FTIR spectroscopy. The dynamic behavior of the azo dyes doped in a series of methacrylate polymers was analyzed in terms of the orientation factors. Two factors, the free volume and the local polarity of matrices, are found to govern the dynamic behavior of DO3. It was found that induced anisotropy for trans and cis isomers varies depending on Tg of polymer matrix. Further, the thermal isomerization rate depend on the isomerization mode which is governed by the matrix polarity. The branched-alkyl chains are considered to block the interaction between ester groups and DO3 and introduce the DO3 molecules into the less polar environment.