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.

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.

NMR analysis of the iron ligand ethylenediaminedi(o-hydroxyphenyl)acetic acid (EDDHA) employed in fertilizers

The exceptional efficiency of the iron chelate of ethylenediaminedi(o-hydroxyphenyl)acetic acid (o,o-EDDHA) in correcting iron chlorosis in plants and the medical applications of various metallic chelates of this compound have long been recognized. As commercial preparations of o,o-EDDHA usually contain impurities, a method for their detection is proposed. By using one- and two-dimensional nuclear magnetic resonance two impurities were identified. The structure of one of these compounds was assigned to an isomer of EDDHA containing at least one p-hydroxyphenyl moiety. The structure of the other impurity was tentatively assigned to a byproduct of the EDDHA synthesis: 2,6-di[CH(COOH)NHCH(2)CH(2)NHCH(COOH)Ar]phenol (Ar = hydroxyphenyl). Both compounds were also detected in the EDDHA extracted from a commercial iron fertilizer.

Relationships between (1)H NMR relaxation data and some technological parameters of meat: a chemometric approach

In this paper chemometrics (ANOVA and PCR) is used to measure unbiased correlations between NMR spin-echo decays of pork M. Longissimus dorsi obtained through Carr-Purcell-Meiboom-Gill (CPMG) experiments at low frequency (20 MHz) and the values of 14 technological parameters commonly used to assess pork meat quality. On the basis of the ANOVA results, it is also found that the CPMG decays of meat cannot be best interpreted with a "discrete" model (i.e., by expanding the decays in a series of a discrete number of exponential components, each with a different transverse relaxation time), but rather with a "continuous" model, by which a continuous distribution of T(2)'s is allowed. The latter model also agrees with literature histological results.

A low frequency 1H-NMR external unit for the analysis of large foodstuff samples

An inexpensive external unit that allows the use of a commercial high-resolution NMR spectrometer as a very low frequency instrument is described. The external unit is phase coherent, the pulse timing being given by the parent spectrometer. With the exception of the probe, the external unit does not contain any tuned elements. This permits easy change of frequency in the range 100 kHz-1 MHz. The external unit may be appropriately employed in food science where, in several cases, low frequency is desirable. An application to hen shell eggs at the frequency of 700 kHz is described.

PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics

The program DYANA, for calculation of solution structures of biomolecules with an algorithm based on simulated annealing by torsion angle dynamics, has been supplemented with a new routine, PSEUDYANA, that enables efficient use of pseudocontact shifts as additional constraints in structure calculations of paramagnetic metalloproteins. PSEUDYANA can determine the location of the metal ion inside the protein frame and allows to define a single tensor of magnetic susceptibility from a family of conformers. As an illustration, a PSEUDYANA structure calculation is provided for a metal-undecapeptide complex, where simulated pseudocontact shifts but no NOE restraints are used as conformational constraints.

Solution structure of the paramagnetic complex of the N-terminal domain of calmodulin with two Ce3+ ions by 1H NMR

The solution structure of the dicerium(III) complex of the N-terminal domain of calmodulin (Ce2-TR1C hereafter) has been solved employing paramagnetic T1 relaxation enhancements and pseudocontact shifts introduced by the Ce3+ ions, together with conventional NOE constraints. The use of pseudocontact shift constraints constitutes the first attempt to locate metal ions within a protein structure by NMR. Like calcium(II), paramagnetic cerium(III) has been found to bind to the two metal binding sites of the TR1C fragment of calmodulin in a cooperative manner. Due to the presence of pseudocontact interactions between the Ce3+ ions and protons of the 76-residue protein, the 1H NMR spectra of the complex show resonances shifted between +22 and -9 ppm. Eighty percent of its proton resonances could be assigned through a standard approach using TOCSY/COSY and NOESY spectra and through 1D NOE difference spectra for the broad resonances of protons close to the paramagnetic ions. A family of structures was calculated by means of the torsion angle dynamics program DYANA [Güntert, P., Mumenthaler, C., & Wüthrich, K. (1996) XVIIthInternational Conference on Magnetic Resonance inBiological Systems (Abstract)] using 1012 NOEs. Longitudinal proton relaxation times helped to roughly define the position of the metal ions within the protein. A total of 381 pseudocontact shift constraints, whose evaluation and use are critically discussed, have then been added to further refine the metal coordinates within the protein frame and to improve the structure resolution. A dramatic resolution improvement of the metal coordinates together with a sizable resolution improvement in the regions close to the paramagnetic centers, where the number of NOEs is low, is observed. The good quality of the solution structure permitted a meaningful comparison with the solid-state structure of calcium-loaded calmodulin at 1.7 A resolution [Chattopadhyaya, R., Meador, W. E., Means, A. R., & Quiocho, F. A. (1992) J. Mol. Biol. 228, 1177]. The Ce2-TR1C complex is overall more compact than the Ca form.

Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins

The pseudocontact shifts of NMR signals, which arise from the magnetic susceptibility anisotropy of paramagnetic molecules, have been used as structural constraints under the form of a pseudopotential in the SANDER module of the AMBER 4.1 molecular dynamics software package. With this procedure, restrained energy minimization (REM) and restrained molecular dynamics (RMD) calculations can be performed on structural models by using pseudocontact shifts. The structure of the cyanide adduct of the Met80Ala mutant of the yeast iso-1-cytochrome c has been used for successfully testing the calculations. For this protein, a family of structures is available, which was obtained by using NOE and pseudocontact shifts as constraints in a distance geometry program. The structures obtained by REM and RMD calculations with the inclusion of pseudocontact shifts are analyzed.

1H NMR of high-potential iron-sulfur protein from the purple non-sulfurbacterium Rhodoferax fermentans

Oxidized and reduced forms of high-potential iron-sulfur protein (HiPIP) from the purple non-sulfur photosynthetic bacterium Rhodoferax fermentans have been characterized using 1H-NMR spectroscopy. Pairwise and sequence-specific assignments of hyperfine-shifted 1H-NMR signals to protons of cysteine residues bound to the [4Fe-4S]3+/2+ cluster have been performed using one-dimensional NOE and exchange spectroscopy experiments. 1H-NMR hyperfine shifts and relaxation rates of cluster-bound Cys beta-CH2 protons indicate that in the [4Fe-4S]3+ cluster one iron ion can be formally described as Fe(III), while electron density corresponding to one electron is unevenly delocalized onto the remaining three iron ions. This delocalization is effected by means of two different electronic distributions interconverting rapidly on the NMR time scale. The mechanism of paramagnetic proton relaxation, studied by analyzing longitudinal relaxation rates of Cys beta-CH2 protons in HiPIPs from six different sources as a function of the Fe-S-C beta-C alpha dihedral angle, indicate that the major contribution is due to a dipolar metal-centered mechanism, with a non-negligible contribution from a ligand-centered dipolar mechanism which involves the 3p orbital of the Cys sulfur atom. A semi-quantitative tool for extracting structural information from relaxation time measurements is proposed.

Inactivation and cleavage of liver 6-P-gluconate dehydrogenase during irradiation in the presence of vanadate

Lamb liver phosphogluconate dehydrogenase is inactivated and selectively cleaved during irradiation in the presence of vanadate. Under our experimental conditions, the correlation between the species of vanadate in solution and rates of enzyme inactivation and cleavage indicates tetravanadate as the most likely photosensitizing agent, in agreement with previous data on other proteins. The enzyme is inactivated more rapidly at acidic pH and is partially protected by the coenzyme NADP, but not by the substrate phosphogluconate. Complete inactivation is obtained when only half of the protein is cleaved into smaller peptides. Differences in the pattern of the peptides produced are observed when irradiation is carried out in phosphate rather than in Hepes buffer: in the former instance cleavage results into formation of a main peptide of 47 kDa, while in latter case two additional peptides of 31 and 25 kDa are produced.