Application of headspace and direct immersion solid-phase microextraction in the analysis of organothiophosphates related to the Chemical Weapons Convention from water and complex matrices.

The successful application of headspace (HS) and direct immersion (DI) solid phase microextraction (SPME) for the unambiguous identification and characterization of a series of toxic thiophosphate esters, such as Amiton (I), from aqueous phases and complex matrices (e.g. grass and foliage) has been demonstrated.

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data.

Mass spectrometry coupled to high-performance liquid chromatography (HPLC-MS) is evolving more quickly than ever. A wide range of different instrument types and experimental setups are commonly used. Modern instruments acquire huge amounts of data, thus requiring tools for an efficient and automated data analysis.

Displacement chromatography as first separating step in online two-dimensional liquid chromatography coupled to mass spectrometry analysis of a complex protein sample--the proteome of neutrophils.

Displacement chromatography provides some advantages over elution chromatography such as the opportunity to enrich trace amounts of molecules and to elute molecules in highest concentrations achievable with liquid chromatography. In a previous study we demonstrated that displacement chromatography is a well-suited alternative to gradient elution in an offline two-dimensional (2D-)LC-MS approach for the analysis of proteomes. In this study we present a method for applying displacement chromatography in an online 2D-LC-MS system including a cation exchange (CEX) column and a reversed phase column.

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine.

OpenMS and TOPP: open source software for LC-MS data analysis.

Proteomics experiments based on state-of-the-art mass spectrometry produce vast amounts of data, which cannot be analyzed manually. Hence, software is needed which is able to analyze the data in an automated fashion. The need for robust and reusable software tools triggered the development of libraries implementing different algorithms for the various analysis steps.

Improved particle-packed HPLC/MS microchips for proteomic analysis.

The influence of packing process parameters (packing pressure, application of ultrasound) and the stationary phase particle size (3.5 and 5 μm) on the chromatographic performance of HPLC/MS chips was systematically investigated for proteomic samples. First, reproducibility and detection limits of the separation were evaluated with a low-complexity sample of tryptic BSA peptides.

BALL--biochemical algorithms library 1.3.

Background: The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers.

Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics.

Targeted proteomic approaches such as multiple reaction monitoring (MRM) overcome problems associated with classical shotgun mass spectrometry experiments. Developing MRM quantitation assays can be time consuming, because relevant peptide representatives of the proteins must be found and their retention time and the product ions must be determined. Given the transitions, hundreds to thousands of them can be scheduled into one experiment run.

Application of displacement chromatography for the analysis of a lipid raft proteome.

Defining membrane proteomes is fundamental to understand the role of membrane proteins in biological processes and to find new targets for drug development. Usually multidimensional chromatography using step or gradient elution is applied for the separation of tryptic peptides of membrane proteins prior to their mass spectrometric analysis. Displacement chromatography (DC) offers several advantages that are helpful for proteome analysis.

De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation.

De novo sequencing of peptides using tandem MS is difficult due to missing fragment ions in the spectra commonly obtained after CID of peptide precursor ions. Complementing CID spectra with spectra obtained in an ion-trap mass spectrometer upon electron transfer dissociation (ETD) significantly increases the sequence coverage with diagnostic ions. In the de novo sequencing algorithm CompNovo presented here, a divide-and-conquer approach was combined with an efficient mass decomposition algorithm to exploit the complementary information contained in CID and ETD spectra.

Application of displacement chromatography for the proteome analysis of a human plasma protein fraction.

It was the aim of this study to compare the performance of displacement chromatography with gradient elution chromatography both applied as the cation-exchange separation step for a proteome analysis in a bottom-up approach using multidimensional chromatography for the separation of tryptic peptides prior to their mass spectrometric analysis. The tryptic digest of the human Cohn fraction IV-4 served as a sample. For both chromatography modes commonly used operating parameters were chosen thus ensuring optimal separation results of equal sample amounts for each mode.

Chemistry of the cephalic labial gland secretions of male Bombus morrisoni and B. rufocinctus, two North American bumblebee males with perching behavior.

The labial gland secretions from males of the North American bumblebees Bombus morrisoni Cresson and B. rufocinctus Cresson were analyzed by gas chromatography/mass spectrometry. In both species, 3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenyl acetate was found as the major compound of a complex mixture of alkenols, acetates, hydrocarbons, and wax-type esters.

OpenMS - an open-source software framework for mass spectrometry.

Background: Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data.

Analysis of the labial gland secretions of the male bumblebee Bombus griseocollis (Hymenoptera: Apidae).

The labial gland secretions from males of the bumblebee Bombus (Separatobombus) griseocollis De Geer, a bumblebee exhibiting perching behaviour, were analysed by gas chromatography/mass spectrometry (GC/MS) in the electron impact and positive ion chemical ionization mode. The major compound of the complex mixture of alkenols, acetates, hydrocarbons, wax type esters and steroids is tetradecyl acetate, considerable amounts of hexadecyl, geranyllinaloyl, geranylgeranyl, docosyl, tetracosenyl and hexacosenyl acetate were also found. 1,3-Tetradecanediol diacetate, detected as a minor component, has not yet been identified in male bumblebee labial gland secretions.

Analysis of the labial gland secretions of the male bumble bee Bombus perplexus Cresson (Hymenoptera: Apidae) from North America.

The labial gland secretions from males of the bumble bee Bombus (Pyrobombus) perplexus Cresson were analysed by gas chromatography/mass spectrometry (GC/MS) in the electron impact and positive ion chemical ionization mode. The major compound of the complex mixture of alkenols, alkenals, fatty acids, hydrocarbons, wax type esters and steroids is 3,7,11,15-tetramethyl-2,6,10-hexadecatrien-1-ol (geranylcitronellol), considerable amounts of hexadecan-1-ol and Z-9-hexadecen-1-ol were also found. All alcohols were present as esters of the detected acids.

Do foraging bumblebees scent-mark food sources and does it matter?

The foraging of worker bees of Bombus terrestris visiting artificial feeders in a climatic test chamber was investigated. The behaviour of worker bees visiting rewarding and unrewarding feeders is completely different. Of all flower visits to rewarding feeders 94% are probing-visits, i.

Foraging in male bumblebees (Bombus lucorum L.): maximizing energy or minimizing water load?

The O, CO, and HO exchange of single flying male bumblebees (Bombus lucorum and B. terrestris) were measured simultaneously. A respiratory quotient RQ=1 was found for all activities investigated (torpor-flight).