Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics.

Mass spectrometry (MS)-based proteomics is a rapidly maturing discipline, thus gaining momentum for routine molecular profiling of clinical specimens to improve disease classification, diagnostics, and therapy development. Yet, hurdles need to be overcome to enhance reproducibility in preanalytical sample processing, especially in large, quantity-limited sample cohorts. Therefore, automated sonication and single-pot solid-phase-enhanced sample preparation (autoSP3) was developed as a streamlined workflow that integrates all tasks from tissue lysis and protein extraction, protein cleanup, and proteolysis. It enables the concurrent processing of 96 clinical samples of any type (fresh-frozen or FFPE tissue, liquid biopsies, or cells) on an automated liquid handling platform, which can be directly interfaced to LC-MS for proteome analysis of clinical specimens with high sensitivity, high reproducibility, and short turn-around times.

Structural and Nutritional Properties of Pasta from Triticum monococcum and Triticum durum Species. A Combined ¹H NMR, MRI, and Digestibility Study.

The aim of the present study was to characterize the structure of two different types of pasta, namely Triticum turgidum ssp. durum (cv. Saragolla) and Triticum monococcum ssp. monococcum (cv. Monlis), under different processing conditions. MRI analysis and NMR spectroscopy (i.e., T1 and T2 NMR relaxation times and diffusion parameters) were conducted on pasta, and (1)H NMR spectroscopic analysis of the chemical compounds released by pasta samples during the cooking process was performed. In addition, starch digestibility (enzimatically determined) was also investigated. The NMR results indicated that Saragolla pasta has a more compact structure, ascribed to pasta network and in particular to different technological gluten properties, that mainly determine the lower ability of Monlis pasta in binding water. These results correlate well with the lower rate of starch hydrolysis measured for Monlis pasta compared to Saragolla when both are dried at high temperature.

Demetalation of Fe, Mn, and Cu chelates and complexes: application to the NMR analysis of micronutrient fertilizers.

The application of nuclear magnetic resonance (NMR) for the quality control of fertilizers based on Fe(3+), Mn(2+), and Cu(2+) chelates and complexes is precluded by the strong paramagnetism of metals. Recently, a method based on the use of ferrocyanide has been described to remove iron from commercial iron chelates based on the o,o-EDDHA [ethylenediamine-N,N'bis(2-hydroxyphenylacetic)acid] chelating agent for their analysis and quantification by NMR. The present work extended that procedure to other paramagnetic ions, manganese and copper, and other chelating, EDTA (ethylenediaminetetraacetic acid), IDHA [N-(1,2-dicarboxyethyl)-d,l-aspartic acid], and complexing agents, gluconate and heptagluconate. Results showed that the removal of the paramagnetic ions was complete, allowing us to obtain (1)H NMR spectra characterized by narrow peaks. The quantification of the ligands by NMR and high-performance liquid chromatography showed that their complete recovery was granted. The NMR analysis enabled detection and quantification of unknown impurities without the need of pure compounds as internal standards.

A quantitative method to assess muscle tissue oxygenation in vivo by monitoring 1H nuclear magnetic resonance myoglobin resonances.

A nuclear magnetic resonance (NMR) method was implemented to assess in vivo oxygenation levels by a quantitative determination of the 1H NMR myoglobin (Mb) resonances. The proximal His-F8 NdeltaH at 70-90 ppm and Val-E11 gammaCH3 resonance at -2.8 ppm, reflecting deoxygenated (deoxy-Mb) and oxygenated (met-Mb) states, were alternately recorded. The method was developed in vitro choosing a couple of NMR sequences that could each maximize the signal-to-noise ratio (SNR) while avoiding baseline rolling and suppressing the water signal. Two quantitative calibration methods were implemented for deoxy- and met-Mb samples (0.1-1 mM), respectively. The respective limit of detection (LOD) and limit of quantification (LOQ) were 0.015 and 0.05 mM for met-Mb and 0.013 and 0.042 mM for deoxy-Mb. Sequences and calibration curves were employed in vivo in Arenicola marina to obtain, for the first time, an accurate measurement of oxy- and deoxy-Mb actual concentrations. In Arenicola, the peaks at approximately 87 and -2.7 ppm, reflecting the deoxy- and oxy-Mb states, respectively, were alternately recorded during increasing hypoxia. The deoxy-Mb concentrations were obtained from the calibration curve. The oxy-Mb concentrations were calculated from the calibration of met-Mb because it was proved that oxy- and met-Mb gave the same NMR molar response. From oxy- and deoxy-Mb concentrations, the intracellular oxygen partial pressure (PiO2) trend was determined.

Water absorption of freeze-dried meat at different water activities: a multianalytical approach using sorption isotherm, differential scanning calorimetry, and nuclear magnetic resonance.

Hydration of freeze-dried chicken breast meat was followed in the water activity range of aw=0.12-0.99 by a multianalytical approach comprising of sorption isotherm, differential scanning calorimetry (DSC), and nuclear magnetic resonance (NMR). The amount of frozen water and the shape of the T2-relaxogram were evaluated at each water content by DSC and NMR, respectively. Data revealed an agreement between sorption isotherm and DSC experiments about the onset of bulk water (aw=0.83-0.86), and NMR detected mobile water starting at aw=0.75. The origin of the short-transverse relaxation time part of the meat NMR signal was also reinvestigated through deuteration experiments and proposed to arise from protons belonging to plasticized matrix structures. It is proved both by D2O experiments and by gravimetry that the extra protons not contributing to the water content in the NMR experiments are about 6.4% of the total proton NMR CPMG signal of meat.

The supramolecular helical architecture of 8-oxoinosine and 8-oxoguanosine derivatives.

The 8-oxoguanosine derivative 1 and the 8-oxoinosine derivative 2 b, with appropriate substituents on their ribose moieties, form hexagonal lyotropic mesophases in hydrocarbon solvents. Small-angle X-ray scattering analysis of a film of 1 and of the mesophase of 2 b, and NMR and CD spectra of isotropic solutions of 2 b, indicate that in both cases the supramolecular structures adopted are continuous helices formed by a hydrogen-bond network between the heterocyclic bases. Notably, while derivative 2 b, which bears large substituents on its ribose moiety, undergoes self-assembly and mesophase formation, oxoinosine 2 a, with only decanoyl groups on its ribose moiety, does not. This may be ascribed to the reduced amphiphilic properties of the latter and the absence of aromatic groups.

A proton NMR relaxation study of hen egg quality.

A quantitative analysis of NMR proton relaxation in hen egg albumen and yolk is undertaken to research the causes of quality loss during the first few days of storage and to access the feasibility of an on-line NMR sensor of internal egg quality. It is shown that the change in the transverse relaxation in thick egg albumen mainly results from an increase in proton exchange rate resulting from a pH increase attributed to loss of carbon dioxide by diffusion through the eggshell. The results suggest that the low-field T1 is the best relaxation time indicator of albumen quality.

Gradient ion-pair chromatographic method for the determination of iron N,N'-ethylenediamine-di-(2-hydroxy-5-sulfophenylacetate) by high performance liquid chromatography-atmospheric pressure ionization electrospray mass spectrometry.

The most effective remedy for iron deficiency is the use of synthetic iron chelates, specifically chelates derived from polyaminecarboxylic acids as EDDHSA (N,N'-ethylenediamine-di-(2-hidroxy-5-sulfophenylacetic) acid). A gradient ion-pair chromatographic method was developed to quantify the total amount of chelated iron in EDDHSA/Fe3+ fertilizers. Two mobile phases were used containing, respectively, 35 and 75% acetonitrile in a 0.005 M tetrabutylammonium hydroxide aqueous solution at pH 6.0. The stationary phase was a reverse phase C-18 column (150mm x 3.9mm i.d., dp = 5 microm). Two chromatographic peaks appeared and were identified by Electrospray Mass Spectrometry. The first peak corresponds to the monomer of EDDHSA/Fe3+ and the second peak has been assigned to condensation molecules. Quality parameters indicate that the method is suitable for the quantification of iron chelate by EDDHSA fertilizers.

Supramolecular helices via self-assembly of 8-oxoguanosines.

The cooperative effect of solvophobic interactions and hydrogen bonding has been exploited to self-assemble supramolecular helical architectures of 8-oxoguanosines in different environments. This self-assembly into helical structures is completely different from that of the parent guanosines which, in the same experimental conditions, form flat, ribbonlike structures. While optical microscopy and X-ray diffraction suggest a chiral columnar aggregate in the LC phase, NMR and Circular Dichroism reveal the presence of a helical structures in solution. Scanning Tunneling Microscopy made it possible to visualize hexagonally arranged G-quartets on graphite, which are sections of the helices packed with their long axis perpendicular to the basal plane of the substrate. Due to their rectifying electrical properties, such helices are interesting for fabricating (opto)electronic biodevices.

Nature of impurities in fertilizers containing EDDHMA/Fe(3+), EDDHSA/Fe(3+), and EDDCHA/Fe(3+) chelates.

Iron chelates derived from ethylenediaminedi(o-hydroxyphenylacetic) acid (EDDHA), ethylenediaminedi(o-hydroxy-p-methylphenylacetic) acid (EDDHMA), ethylenediaminedi(2-hydroxy-5-sulfophenylacetic) acid (EDDHSA), and ethylenediaminedi(5-carboxy-2-hydroxyphenylacetic) acid (EDDCHA) are remarkably efficient in correcting iron chlorosis in plants growing in alkaline soils. This work reports the determination of impurities in commercial samples of fertilizers containing EDDHMA/Fe(3+), EDDHSA/Fe(3+), and EDDCHA/Fe(3+). The active components (EDDHMA/Fe(3+), EDDHSA/Fe(3+), and EDDCHA/Fe(3+)) were separated easily from other compounds present in the fertilizers by HPLC. Comparison of the retention times and the UV-visible spectra of the peaks obtained from commercial EDDHSA/Fe(3+) and EDDCHA/Fe(3+) samples with those of standard solutions showed that unreacted starting materials (p-hydroxybenzenesulfonic acid and p-hydroxybenzoic acid, respectively) were always present in the commercial products. 1D and 2D NMR experiments showed that commercial fertilizers based on EDDHMA/Fe(3+) contained impurities having structures tentatively assigned to iron chelates of two isomers of EDDHMA. These findings suggest that current production processes of iron chelates used in agriculture need to be improved.