Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data

The quantity and variable quality of data that can be generated from liquid chromatography (LC)/mass spectrometry (MS)-based proteomics analyses creates many challenges in interpreting the spectra in terms of the actual proteins in a complex sample. In spite of improvements in algorithms that match putative peptide sequences to MS/MS spectra, the assembly of these lists of possible or probable peptides into a 'correct' set of proteins is still problematic. We have observed a trend in a simple relationship, derived from standard database search outputs, which can be useful in assessing the quality of a MS/MS-based protein identification. Specifically, the ratio of the protein score and number of non-redundant peptides, or average peptide score (APS), can facilitate initial filtering of database search results in addition to providing a useful measure of confidence for the proteins identified. This parameter has been applied to results from the analysis of multi-protein complexes derived from pull-down experiments analyzed using a two-dimensional LC/MS/MS workflow. In particular, the complex list of protein identifications derived from a drug affinity pull-down with immobilized ampicillin and an E. coli lysate was greatly simplified by applying the APS as a filter, allowing for facile identification of the penicillin-binding proteins known to interact with ampicillin. Furthermore, an APS threshold can be used for any data sets derived from electrospray ionization (ESI)- or matrix-assisted laser desorption/ionization (MALDI)-MS/MS experiments and is also not specific to any database search program.     

A variational proof of the Gauss-Bonnet formula

The classical Gauss-Bonnet formula has the form I(g_ij)=2, where I(g_ij) represents a sum of three terms each of which depends on the metric tensor g_ij. It is shown that the first variation I of I(g_ij) with respect to the metric g_ij vanishes and that for the Euclidean metric _ij we have I(_ij)=2. From this the formula I(g_ij)=2 follows. In the process, explicit expressions are obtained for the first variation of each of the three terms which comprise I(g_ij). Furthermore, a general expression for the first variation of a multiple integral whose integrand is a scalar density depending on the metric tensor g_ij and its derivatives up to the second order is obtained with the aid of results of Rund [1].     

Ternäre Halogenide der Seltenen Erden vom Typ A2MX5 (A = K,In, NH4, Rb,Cs; X = Cl,Br, I)

Ternary Rare-Earth Halides of the A₂MX₅ Type (A = K, In, NH₄, Rb, Cs; X = Cl, Br, I) Ternary rare-earth (=M) chlorides, bromides, and iodides In₂MCl₅, (NH₄)₂MCl₅, Rb₂MCl₅, Cs₂MCl₅, CsRbMCl₅, K₂MBr₅, Rb₂MBr₅, K₂MI₅, and Rb₂MI₅ have been synthesized. Single crystals of In₂PrCl₅, Rb₂PrCl₅, K₂PrBr₅, and K₂PrI₅ were grown and the structures refined. The other halides were characterized by x-ray powder patterns. They are isotypic either with K₂PrCl₅(orthorhombic, Pnma, Z = 4, hexagonal arrangement of chains of edge-connected polyhedra [PrX₇]) or with Cs₂DyCl₅ (orthorhombic, Pbnm, Z = 4, hexagonal arrangement of cis-corner-connected octahedra [DyCl₆]) which may be discriminated in structure field diagrams. The thermal expansion was investigated für Cs₂LuCl₅ and Rb₂PrX₅ (X = Cl, Br, I).     

Application of capillary reversed-phase high-performance liquid chromatography to high-sensitivity protein sequence analysis.

A continuous gradient elution method for capillary column (less than 0.32 mm I.D.) liquid chromatography was developed. Gradient eluent from a microbore liquid chromatograph was split ahead of the injector so that an accurate percentage (2-3%) of the mobile phase delivered by the pump flowed through the capillary column. The outlet of the column was connected to a length of 0.075 mm I.D. fused-silica capillary tubing which, in turn, was connected to a 6-mm optical path length longitudinal capillary flow cell. Fused-silica capillary columns of 0.32 mm I.D. were slurry-packed efficiently with 7-microns spherical, 300 A pore size, C8 bonded-phase particles, and evaluated in terms of their ability to resolve mixtures of proteins, peptides or phenylthiohydantoin (PTH)-amino acid derivatives. The gradient elution profiles agreed with those obtained using microbore (less than 2.1 mm I.D.) and larger bore columns. The minimum detectable amounts for proteins and PTH-amino acids on 0.32 mm I.D. capillary columns were 50 pg and 25 fmol, respectively. At a flow-rate of 3.6 microliters/min, proteins and peptides were recovered from the capillary columns in volumes of about 2-8 microliters. The use of a multiple-wavelength, forward-optics detector for identifying tryptophan- and tyrosine-containing peptides is discussed.     

Laser-induced electron impact ionization in a reflectron time-of-flight mass spectrometer

Some details of the generation of electrons by impinging a laser beam on a metal surface are described. It is shown that highly efficient electron generation is observed only during the laser pulse. Therefore, this technique delivers intense pulses of electrons. The process is investigated and different ion source set-ups are discussed. In conjunction with a time-of-flight mass spectrometer this technique can be used to produce mass spectra of different samples ranging from simple organic molecules to peptides.     

Iodometric determination of ferricyan in the presence of copper,silver, cadmium and zinc

Ferricyan can be determined in the presence of copper, silver and cadmium by addition of potassium ferrocyanide, filtration of the ferrocyanides of copper, silver and cadmium formed in this reaction, and titration of the potassium ferricyanide contained in the filtrate. In the case of silver, the ferricyan can also be determined without filtration by addition of potassium iodide and titration of the ferricyanide. In the case of zinc, potassium, ferrocyanide is added and without filtration the ferricyanide titrated.     

Ring-fused cyclobutanes via cycloisomerization of alkylidenecyclopropane acylsilanes

A novel Lewis acid-catalyzed cycloisomerization of alkylidenecyclopropane acylsilanes is disclosed. The readily available starting materials participate in tandem Prins addition/ring expansion/1,2-silyl shift to grant access to bicyclo[4.2.0]octanes and bicyclo[3.2.0]heptanes, which are common motifs in terpenoid natural products. Notably, the transformation relies on the ability of acylsilanes to act sequentially as acceptors and donors on the same carbon atom.

A novel Lewis acid-catalyzed cycloisomerization of alkylidenecyclopropane acylsilanes is disclosed that involves tandem Prins addition/ring expansion/1,2-silyl shift to grant access to bicyclo[4.2.0]octanes and bicyclo[3.2.0]heptanes.