Post-acquisition ETD spectral processing for increased peptide identifications

Tandem mass spectra (MS/MS) produced using electron transfer dissociation (ETD) differ from those derived from collision-activated dissociation (CAD) in several important ways. Foremost, the predominant fragment ion series are different: c- and z ^·-type ions are favored in ETD spectra while b- and y-type ions comprise the bulk of the fragments in CAD spectra. Additionally, ETD spectra possess charge-reduced precursors and unique neutral losses. Most database search algorithms were designed to analyze CAD spectra, and have only recently been adapted to accommodate c- and z ^·-type ions; therefore, inclusion of these additional spectral features can hinder identification, leading to lower confidence scores and decreased sensitivity. Because of this, it is important to pre-process spectral data before submission to a database search to remove those features that cause complications. Here, we demonstrate the effects of removing these features on the number of unique peptide identifications at a 1% false discovery rate (FDR) using the open mass spectrometry search algorithm (OMSSA). When analyzing two biologic replicates of a yeast protein extract in three total analyses, the number of unique identifications with a ∼1% FDR increased from 4611 to 5931 upon spectral pre-processing—an increase of ∼28. 6%. We outline the most effective pre-processing methods, and provide free software containing these algorithms.     

Auxiliary probe design adaptable to existing probes for remote detection NMR, MRI, and time-of-flight tracing

A versatile, detection-only probe design is presented that can be adapted to any existing NMR or MRI probe with the purpose of making the remote detection concept generally applicable. Remote detection suggests freeing the NMR experiment from the confinement of using the same radio frequency (RF) coil and magnetic field for both information encoding and signal detection. Information is stored during the encoding step onto a fluid sensor medium whose magnetization is later measured in a different location. The choice of an RF probe and magnetic field for encoding can be made based solely on the size and characteristics of the sample and the desired information quality without considering detection sensitivity, as this aspect is dealt with by a separate detector. While early experiments required building probes that included two resonant circuits, one for encoding and one for detection, a modular approach with a detection-only probe as presented here can be used along with any existing NMR probe of choice for encoding. The design of two different detection-only probes is presented, one with a saddle coil for milliliter-sized detection volumes, and the other one with a microsolenoid coil for sub-microliter fluid quantities. As example applications, we present time-of-flight (TOF) tracing of hyperpolarized (129)Xe spins in a gas mixture through coiled tubing using the microsolenoid coil detector and TOF flow imaging through a nested glass container where the gas flow changes its direction twice between inlet and outlet using the saddle coil detector.     

Measurement of radon concentrations and their annual effective doses in soils and rocks of Jaintiapur and its adjacent areas,Sylhet, North-east Bangladesh

Journal of Radioanalytical and Nuclear Chemistry - The study investigates the measurement of radon concentration in soils and rocks as a natural tracer for exploring uranium mineralization, first...     

P to Se cross polarization in β-P4Se3

Cross polarization from ³¹P to ⁷⁷Se is demonstrated in β-P₄Se₃. This material, an inorganic glass, is readily synthesized from the elements and serves as a convenient sample for setting the Hartmann-Hahn condition.     

Regular groups on generalized quadrangles and nonabelian difference sets with multiplier -1

This is a first approach to the study of regular generalized quadrangles (i.e. generalized quadrangles with an automorphism group sharply 1-transitive on points). In this paper we point out how the problem is connected to the theory of difference sets with multiplier-1. First, some of the results in [3] on difference sets with multiplier-1 are extended to the nonabelian case; then, these new results on difference sets are used to prove nonexistence theorems for regular GQs of even order s=t.Dedicated to Otto Wagner on the occasion of his 60th birthday     

Extended partial geometries with minimal μ

Recently Fisher and Hobart extended the original work of Buekenhout and Hubaut on extended generalized quadrangles with a certain minimal value (minimal ) for the nonempty residue intersections. We show that there is another minimal which is sometimes better than the earlier one, and we extend all this to the case of extended partial geometries. We examine especially the triangular case, and find only a few new possibilities, which we are unable to settle, although some of these look extremely interesting.