Investigation of sample-purification procedures for MALDI-based proteomic studies

Purification methods for proteomics samples are of crucial concern for improving the quality of the sample delivered to the mass spectrometer. They constitute the link between the mass spectrometer and protein processing and peptide isolation steps that usually require solvents, buffers, or detergents completely incompatible with MS-analysis conditions. This work describes three new clean-up procedures using synthetic membranes and polymer media and compares them with standard procedures. The efficiency of each of the purification procedures was studied via application to four standards and two membrane proteins. This work highlights the importance of versatility in sample preparation, especially for MS-based proteomic investigations. Figure PMF spectra obtained after MALDI-TOF measurements of bovine mitochondrial complex III (A) and complex IV (B) in-solution digests, with and without purification     

DNA-based phosphane ligands

In order to expand the repertoire of DNA sequences specifically interacting with transition metals, we report here the first examples of DNA sequences carrying mono- and bidentate phosphane ligands as well as P,N-ligands. Aminoalkyl-modified oligonucleotides have been reacted at predetermined internal sites with carboxylate derivatives of pyrphos, BINAP and phosphinooxazoline (PHOX) 2 b-d. Carbodiimide coupling in the presence of N-hydroxysuccinimide provided the DNA-ligand conjugates in 38-78 % yield. Phosphane-containing oligonucleotides and their phosphane sulfide analogues were characterized by mass spectrometry (MALDI-TOF and FT-ICR-ESI) and their stability after purification and isolation was systematically investigated. While DNA-appended pyrphos ligand was quickly oxidized, BINAP and PHOX conjugates showed high stabilities, making them useful precursors for incorporation of transition metals into DNA.     

Self-assembly reactions between the cis-protected metal corners (N-N)MII (N-N = ethylenediamine, 4,4'-substituted 2,2'-bipyridine; M = Pd, Pt) and the fluorinated edge 1,4-bis(4-pyridyl)tetrafluorobenzene

The self-assembly reactions between the fluorinated ditopic ligand 1,4-bis(4-pyridyl)tetrafluorobenzene (A) and different nitrogen-protected palladium(II) and platinum(II) complexes have been investigated. While dynamic equilibria between molecular triangles and squares were observed when the diimine compounds 4,4'-R2bipy (bipy = 2,2'-bipyridine; R = H, Me, t-Bu) were employed as ancillary ligands, only square species were obtained from ethylenediamine (en) derivatives. Characterization of the obtained metallomacrocycles was accomplished by 1H and 19F NMR spectroscopy in combination with electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR). Molecular dynamics simulations (UFF) have been performed to interpret the influence of the fluorinated ring on the square/triangle relative stability. Density functional calculations using the GIAO method have been employed for the interpretation of the chemical shift assignments. The study of the ability of these compounds to act as hosts of electron-rich aromatic guests has shown that the palladium ethylenediamine square is capable of establishing this type of intermolecular interaction exclusively in aqueous media. The host-guest stoichiometry and association constants have been determinated by 1H NMR spectroscopy.     

Structural Properties Governing Retention Mechanisms on Immobilized Artificial Membrane (IAM) HPLC Columns

The aims of this study were to investigate whether three commercially available immobilized artificial membrane (IAM) HPLC columns yield collinear data for neutral compounds, and whether IAM scales are distinct from the log P_oct (partition coefficient in the octanol/H₂O system) scale. With these objectives, the retention mechanisms on the IAM HPLC columns were analysed by linear solvation free‐energy relationships (LSERs). A set of 68 neutral model compounds with known solvatochromic parameters and log P_oct values was investigated, allowing a regular and broad exploration of property space. The resulting solvatochromic equations clearly indicate that the three IAM stationary phases retain small neutral solutes by a balance of intermolecular forces closely resembling those underlying partitioning in octanol/H₂O and retention on a reversed‐phase LC‐ABZ HPLC column. For all systems, the solute's size and hydrogen‐bond‐acceptor basicity are the two predominant factors, whereas dipolarity/polarisability and hydrogen‐bond‐donor acidity play only minor roles.     

Analysis of thermograms for the estimation of dimensions of cracks in building envelope

In situ determination of global air leakage of the building envelope is presently done with the fan depressurization test. During such test, infrared thermography could also be used to dimension unintentional small openings (cracks). In this study, thermography was used to measure in laboratory the surface temperature of single-layer walls subjected to air flow through surrogates of cracks. Two image-processing methods were developed and applied to a dataset of 36 thermograms recorded in laboratory. First, using the edge detection technique, the opening length and large width (more than 4 mm) can be graphically estimated with an error of less than 8%. Second, for smaller openings, correlations for two image-processing characteristics, peak height and missing attenuation, were established. These relationships result in estimation with a relative error of less than 4% of the widths of small cracks on thermograms. The development of correlations for the spectrum of conditions found on site could be a step towards in situ quantification of air leakage areas.     

The geometries of coadsorbate layers of O and H on Ru(0 0 1): How well can quantitative LEED see hydrogen atoms?

Using a CCD LEED system for the collection of IV data with low beam damage, and full dynamical as well as tensor LEED calculations, we have determined the geometries of the (2 × 2)-(O + 3H) and the (2 × 2)-(O + H) coadsorbate structures on Ru(0 0 1). We show that here quantitative LEED can locate the H atoms very well. Not only their sites (hcp in the first, fcc in the second case), but also the Ru–H spacings and changes in the first two substrate layers are clearly determined. We argue that this success is due to the relatively large data range and to the smaller H mobility compared to pure H layers caused by their repulsive lateral interactions with the oxygen atoms.     

Hybridization of Nafion membranes with an acid functionalised polysiloxane: Effect of morphology on water sorption and proton conductivity

Polysiloxane-modified hybrid Nafion membranes were prepared by casting a mixture of Nafion solution and a precursor of acid functionalised polysiloxane based on tetraethoxysilane and a mercaptan-organoalkoxysilane.Scanning Electron Microscopy (SEM) and Atomic Force Microscopy analysis revealed that the functionalised polysiloxane was dispersed either as finely nanosized inclusions or as coarse domains depending on the rate of the solvent evaporation during the casting procedure. In particular the slower is the rate of solvent evaporation the more interpenetrated and homogenously dispersed at nanosized level is the polysiloxane inside the Nafion membrane.The hybridization process increases the thermal stability of the membranes of about 50 °C relatively to the unmodified Nafion. Small angle X-ray scattering (SAXS) analysis reveals that the hybrid membranes exhibited the typical morphology of Nafion consisting of distinct hydrophilic and hydrophobic domains.Water vapor sorption and proton conductivity were measured varying the temperature (up to 120 °C) and the water activity conditions (from 0.1 to 0.8). The polysiloxane network always increases the water vapor uptake of the membranes and increases significantly the proton conductivity at higher temperature depending on the type of morphology developed by the manufacturing method. In particular hybrid membranes exhibiting nanosized polysiloxane dispersion show a proton conductivity which is up to one-and-half time higher than Nafion recast membrane at high temperature and low water content.     

Controlled/living radical polymerization of isoprene and butadiene in emulsion

A process for RAFT-controlled radical polymerization in emulsion [36] has been applied to the polymerizations of isoprene and of butadiene in emulsion systems, with the goal of producing latex particles containing block copolymers of acrylic acid (stabilizer and starting polymer), styrene (second polymer) and isoprene or butadiene (third polymer). The microstructure of the polymer chains was examined using dual-detection size-exclusion chromatography, and the nanostructure of the materials was investigated by differential scanning calorimetry and solid-state nuclear magnetic resonance. Reactions were always slow (although faster than the corresponding processes in solution), and exhibited limited reinitiation by isoprene when in emulsion. The materials containing isoprene exhibit a nanostructure with a phase separation into high-T_g polystyrene-rich domains and low-T_g polyisoprene-rich domains, revealed by DSC and NMR. This has the potential to lead to barrier materials with novel physical properties.     

Degradation of ionized OV(OCH3)3 in the gas phase. From the neutral compound all the way down to the quasi-terminal fragments VO+ and VOH+

The consecutive fragmentation of ionized trimethyl vanadate(V), OV(OCH3)3 (1), is examined by experiment and theory. After an elimination of formaldehyde from the molecular ion 1+, subsequent dissociations proceed via losses of first H2 and then two molecules of formaldehyde to finally yield the VOH+ cation; these redox reactions involve the V(II)/V(IV) manifold. At elevated energies, expulsion of CH3O* from 1+ can efficiently compete to afford OV(OCH3)2+, a formal V(V) compound, from which subsequent losses of H2 and two units of CH2O lead to bare VO+, thereby exploring the V(III)/V(V) redox manifold. Experiments using complementary mass spectrometric techniques, i.e., neutralization-reionization experiments and ion/molecule reactions, in conjunction with extensive computational studies provide deep insight into the ion structures and the relative energetics of these dissociation reactions. In particular, a quantitative energetic scheme is obtained that ranges from neutral OV(OCH3)3 all the way down to the quasi-terminal fragment ions VOH+ and VO+, respectively.     

Nonaqueous capillary electrophoresis method for the enantiomeric purity determination of S-timolol using heptakis(2,3-di-O-methyl-6-O-sulfo)-beta-cyclodextrin: validation using the accuracy profile strategy and estimation of uncertainty

Nonaqueous capillary electrophoresis (NACE) was successfully applied to the enantiomeric purity determination of S-timolol maleate using heptakis(2,3-di-O-methyl-6-O-sulfo)-beta-cyclodextrin (HDMS-beta-CD) as chiral selector. With a background electrolyte made up of a methanolic solution of 0.75 M formic acid, 30 mM potassium camphorsulfonate and containing 30 mM HDMS-beta-CD, the determination of 0.1% of R-timolol in S-timolol could be performed with an enantiomeric resolution of 8.5. Pyridoxine was selected as internal standard. The NACE method was then fully validated by applying a novel strategy using accuracy profiles. It is based on beta-expectation tolerance intervals for the total measurement error which includes trueness and intermediate precision. The uncertainty of measurements derived from beta-expectation tolerance intervals was estimated at each concentration level of the validation standards. To confirm the suitability of the developed and validated method, several real samples of S-timolol maleate containing R-timolol maleate at different concentrations were analysed and the results were compared to those obtained by liquid chromatography.