Collision cell pressure effect on CID spectra pattern using triple quadrupole instruments: a RRKM modeling

Control of the ion internal energy in mass spectrometry is needed to establish a workable mass spectral library. The purpose of this study is to understand and to compare the pressure effects on the collision‐induced dissociation (CID) spectrum pattern recorded using triple quadrupole instruments. The monoprotonated Leucine enkephalin [YGGFL, H⁺] was used as a thermometer molecule to calibrate the electrospray ionization (ESI) and the CID internal energies deposited on the molecular species and the time scale of ion decompositions. The survival yield and the ratio of a₄/b₄ fragment ions were mainly monitored. The energy uptake for the ESI source geometry used in our study has no impact on the CID spectrum fingerprint. The collision cell pressure for the [YGGFL, H⁺] has a major influence on the SY curves slope and on the experimental time scale. To demonstrate the pressure effect on internal energy distribution, three models (threshold, thermal and collisional) based on RRKM theory were built using the Masskinetics software. As a result, the limit of each model is discussed, and the investigation demonstrates that the thermal model, using truncated Maxwell‐Boltzmann internal energy distribution, is well‐suited for simulating the experimental data at high pressure widely used in the analytical conditions. Copyright © 2013 John Wiley & Sons, Ltd.     

N-Glycosidase treatment with 18O labeling and de novo sequencing argues for flagellin FliC glycopolymorphism in Pseudomonas aeruginosa

In prokaryote organisms, N-glycosylation of proteins is often correlated to cell–cell recognition and extracellular events. Those glycoproteins are potential targets for infection control. To date, many surface-glycosylated proteins from bacterial pathogens have been described. However, N-linked Pseudomonas surface-associated glycoproteins remain underexplored. We report a combined enrichment and labeling strategy to identify major glycoproteins on the outside of microorganisms. More precisely, bacteria were exposed to a mix of biotinylated lectins able to bind with glycoproteins. The latter were then recovered by avidin beads, digested with trypsin, and submitted to mass spectrometry. The targeted mixture of glycoproteins was additionally deglycosylated in the presence of H₂ ¹⁸O to incorporate ¹⁸O during PNGase F treatment and were also analyzed using mass spectrometry. This approach allowed us to identify a few tens of potential N-glycoproteins, among which flagellin FliC was the most abundant. To detect the possible sites of FliC modifications, a de novo sequencing step was also performed to discriminate between spontaneous deamidation and N-glycan loss. This approach led to the proposal of three potential N-glycosylated sites on the primary sequence of FliC: N26, N69, and N439, with two of these three asparagines belonging to an N-X-(S/T) consensus sequence. These observations suggest that flagellin FliC is a heterogeneous protein mixture containing both O- and N-glycoforms.

QMX: A versatile environment for hybrid calculations applied to the grafting of Al2Cl3Me3 on a silica surface

We present a new software to easily perform QM:MM and QM:QM' calculations called QMX. It follows the subtraction scheme and it is implemented in the Atomic Simulation Environment (ASE). Special attention is paid to couple molecular calculations with periodic boundaries approaches. QMX inherits the flexibility and versatility of the ASE package: any combination of methods namely force field, semiempirical, first principle, and ab initio, can be used as hybrid potential energy surface (PES). Its ease of use is demonstrated by considering the adsorption of Al₂Cl₃Me₃ on silica surface and by combining different levels of theory (from standard DFT to MP2 calculations) for the so‐called High Level cluster with standard PW91 density functional theory calculations for the Low Level environment. It is shown that the High Level cluster must contain the silanol group close to the aluminum atoms. The bridging adsorption is favored by 58 kJ mol^?1 at the MP2:PW91 level with respect to the terminal position. Using large clusters at the MP2:PW91 level, it is shown that PW91 calculations are sufficient for structure optimization but that embedded methods are required for accurate energy profiles. © 2013 Wiley Periodicals, Inc.     

Proposed terminology of ‘lato sensu metrology’ for scientific methodology

Currently, there are two international scientific vocabularies devoted to properties: one dealing on quantities and the other one dealing on nominal properties. In this article, I am proposing the two mentioned vocabularies be merged in order to make available most of the basic concepts, terms, and definitions needed in observational and experimental scientific methodology in a single vocabulary. In addition, I propose the provisional use of the term “lato sensu metrology” to describe the new vocabulary.     

Three new monoterpene indole alkaloids from Psychotria umbellata Thonn.

Three new psychollatine-derived monoterpene indole alkaloids were obtained from Psychotria umbellata Thonn.: 3,4-Dehydro-18,19-β-epoxy-psychollatine (2), N⁴-[1-((R)-2-hydroxypropyl)]-psychollatine (3), and N⁴-[1-((S)-2-hydroxypropyl)]-psychollatine (4). Their structures were determined by ¹H and ¹³C NMR spectra, 2D correlations (COSY, HMQC, and HMBC), and mass and UV spectra. Compounds 3 and 4 were synthesized for structural confirmation and for the determination of the stereochemistry of the hydroxyl group.     

Experimental and Monte Carlo simulation on new manganese bath facility for absolute neutron source emission rate measurement at ENEA-INMRI

This work deals with the absolute measurement of the neutron emission rate from a ²⁴¹Am–Be source by means of the manganese sulphate bath technique, which is the principal method for the absolute determination of the neutron emission rate from radionuclide neutron sources. The facility consists of a spherical container filled with an aqueous solution of manganese sulphate with a ²⁴¹Am–Be neutron source placed at the center. As well known, neutrons from the source, after having been thermalized by the aqueous solution, undergo neutron capture by hydrogen, manganese, sulphur, and oxygen nuclei, thus inducing a certain activity to the solution. Subsequent gamma spectrometry measurements of ⁵⁶Mn activity generated by ⁵⁵Mn neutron activation allows to determine the neutron emission rate of the source, The experimental activity has involved a variety of measurement techniques and calculation procedures, ranging from neutron reactor activation to liquid scintillation counting and Monte Carlo calculations. Neutron activations of ⁵⁵Mn samples has been carried out with the TRIGA reactor of the ENEA-Casaccia Research Centre, and ⁵⁶Mn activated samples were subsequently characterized by liquid scintillation counting, in order to obtain reference standards for the calibration of the NaI(Tl) scintillation detectors utilized to record gamma-ray emission from ⁵⁶Mn. Monte Carlo calculations, carried out by the MCNPX code, were required to calculate neutron transport within the sulphate manganese bath, in particular to determine ⁵⁵Mn neutron capture probability, and (n, α) and (n, p) concurrent reactions, as well as the neutron leakage. Such a procedure has allowed to maintaining the neutron emission rate uncertainty well below 1 %. All the measurements have been carried out at the ENEA-Casaccia Research Centre by the Italian National Institute of Ionizing Radiation Metrology.