High Abundance of Unusual High Mannose -Glycans Found in Beans.

High mannose -glycans extracted from eight different beans (black bean, soybean, pea, white kidney bean, pinto bean, mung bean, white hyacinth bean, and red bean) were studied using the state-of-the-art mass spectrometry method logically derived sequence tandem mass spectrometry (LODES/MS). These beans show very similar -glycan isomer profiles: one isomer of ManGlcNAc and ManGlcNAc, two isomers of ManGlcNAc, three isomers of ManGlcNAc, and five isomers of ManGlcNAc were found. Isomers not predicted by current -glycan biosynthetic pathways were found in all beans, indicating the possibility of alternative biosynthetic pathways in these plants.

Collision-Induced Dissociation of Fucose and Identification of Anomericity.

Structural determination of carbohydrates using mass spectrometry remains challenging, particularly, the differentiation of anomeric configurations. In this work, we studied the collision-induced dissociation (CID) mechanisms of sodiated α- and β-l-fucose using an experimental method and quantum chemistry calculations. The calculations show that α-l-fucose is more likely to undergo dehydration due to the fact that O1 and O2 are on the same side of the sugar ring.

Chromatograms and Mass Spectra of High-Mannose and Paucimannose -Glycans for Rapid Isomeric Identifications.

-Linked glycosylation is one of the most essential post-translational modifications of proteins. However, -glycan structural determination remains challenging because of the small differences in structures between isomers. In this study, we constructed a database containing collision-induced dissociation MS mass spectra and chromatograms of high-performance liquid chromatography for the rapid identification of high-mannose and paucimannose -glycan isomers.

Identification of side-reaction products generated during the ammonia-catalyzed release of N-glycans.

N-linked glycosylation is one of the most important post translational modification of proteins. Various analytical techniques are used for the structural identification of the N-glycans released from proteins through various enzymatic and chemical methods. Although very few side-reaction products are generated during the enzymatic release of N-glycans, this method is expensive and suitable only for small quantities of samples.

Electrospray ionization in-source decay of N-glycans and the effects on N-glycan structural identification.

Rational: Electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) are soft ionization techniques commonly used in mass spectrometry. Although in-source and post-source decays of MALDI have been investigated extensively, the analogous decays of ESI have received little attention. Previous studies regarding the analogous decays of ESI focus on the dissociation of multiply charged proteins and peptides.

Collision-induced dissociation of xylose and its applications in linkage and anomericity identification.

Collision-induced dissociation (CID) of α-xylose and β-xylose were studied using mass spectrometry and quantum chemistry calculations. Three dissociation channels, namely loss of metal ions, dehydration, and cross-ring dissociation were found. The major dissociation channel of sodium adducts is the loss of sodium ions, and the minor dissociation channels are dehydration and cross-ring dissociation.

Unexpected Dissociation Mechanism of Sodiated N-Acetylglucosamine and N-Acetylgalactosamine.

The mechanism for the collision-induced dissociation (CID) of two sodiated N-acetylhexosamines (HexNAc), N-acetylglucosamine (GlcNAc), and N-acetylgalactosamine (GalNAc), was studied using quantum-chemistry calculations and resonance excitation in a low-pressure linear ion trap. Experimental results show that the major dissociation channel of the isotope labeled [1-O, D]-HexNAc is the dehydration by eliminating HDO, where OD comes from the OD group at C3. Dissociation channels of minor importance include the A cross-ring dissociation.

Toward understanding the ionization mechanism of matrix-assisted ionization using mass spectrometry experiment and theory.

Rationale: Matrix-assisted ionization (MAI) mass spectrometry does not require voltages, a laser beam, or added heat to initiate ionization, but it is strongly dependent on the choice of matrix and the vacuum conditions. High charge state distributions of nonvolatile analyte ions produced by MAI suggest that the ionization mechanism may be similar to that of electrospray ionization (ESI), but different from matrix-assisted laser desorption/ionization (MALDI). While significant information is available for MAI using mass spectrometers operating at atmospheric and intermediate pressure, little is known about the mechanism at high vacuum.

Collision-induced dissociation of sodiated glucose, galactose, and mannose, and the identification of anomeric configurations.

Collision-induced dissociation of sodiated α-glucose, β-glucose, α-galactose, β-galactose, α-mannose, and β-mannose was studied using electronic structure calculations and resonance excitation in a low-pressure linear ion trap. We made an extensive search of conformers and transition states in calculations to ensure the transition state with the lowest barrier height for each dissociation channel could be located. The major dissociation channels, in addition to desodiation, are cross-ring dissociation and dehydration.

Does low-energy collision-induced dissociation of lithiated and sodiated carbohydrates always occur at anomeric carbon of the reducing end?

Rationale: Collision-induced dissociation (CID) tandem mass spectrometry is one of the major methods in the structural determination of carbohydrates. Previous experimental studies and theoretical investigation of lithiated and sodiated underivatized carbohydrates seem to indicate that dehydration reactions and cross-ring dissociation of low-energy CID mainly occur at the anomeric carbon of the reducing end. However, these studies only investigated a few carbohydrates.

Laser Pulse Width Dependence and Ionization Mechanism of Matrix-Assisted Laser Desorption/Ionization.

Ultraviolet laser pulses at 355 nm with variable pulse widths in the region from 170 ps to 1.5 ns were used to investigate the ionization mechanism of matrix-assisted laser desorption/ionization (MALDI) for matrices 2,5-dihydroxybenzoic acid (DHB), α-cyano-4-hydroxycinnamic acid (CHCA), and sinapinic acid (SA). The mass spectra of desorbed ions and the intensity and velocity distribution of desorbed neutrals were measured simultaneously for each laser shot.

Collision-induced dissociation of sodiated glucose and identification of anomeric configuration.

Collision-induced dissociation (CID) of sodiated glucose was investigated using electronic structure calculations and resonance excitation in a low-pressure linear ion trap. The major dissociation channels in addition to desodiation are dehydration and CHO elimination reactions which the barrier heights are near to or lower than the sodiation energy of glucose. Dehydration reaction involves the transfer of the H atom from the O2 atom to the O1 atom, followed by the cleavage of the C1-O1 bond.

Comment on: MALDI ionization mechanisms investigated by comparison of isomers of dihydroxybenzoic acid.

Ionization mechanism of matrix-assisted laser desorption/ionization was recently investigated by Kirmess et al. (J. Mass Spectrom.

Highly Selective Dissociation of a Peptide Bond Following Excitation of Core Electrons.

The controlled breaking of a specific chemical bond with photons in complex molecules remains a major challenge in chemistry. In principle, using the K-edge absorption of a particular atomic element, one might excite selectively a specific atomic entity in a molecule. We report here highly selective dissociation of the peptide bonds in N-methylformamide and N-methylacetamide on tuning the X-ray wavelength to the K-edge absorption of the atoms connected to (or near) the peptide bond.

Ion-to-Neutral Ratios and Thermal Proton Transfer in Matrix-Assisted Laser Desorption/Ionization.

The ion-to-neutral ratios of four commonly used solid matrices, α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (2,5-DHB), sinapinic acid (SA), and ferulic acid (FA) in matrix-assisted laser desorption/ionization (MALDI) at 355 nm are reported. Ions are measured using a time-of-flight mass spectrometer combined with a time-sliced ion imaging detector. Neutrals are measured using a rotatable quadrupole mass spectrometer.

Core excitation, specific dissociation, and the effect of the size of aromatic molecules connected to oxygen: phenyl ether and 1,3-diphenoxybenzene.

Near-edge X-ray absorption fine structure (NEXAFS) spectra of phenyl ether at the carbon K-edge and 1,3-diphenoxybenzene at both the carbon and oxygen K-edges were measured in the total ion yield mode using X-rays from a synchrotron and a reflectron time-of-flight mass spectrometer. Time-dependent density functional theory was adopted to calculate the carbon and oxygen K-edge NEXAFS spectra of phenol, phenyl ether, and 1,3-diphenoxybenzene. The assignments and a comparison of the experimental and calculated spectra are presented.

Theoretical prediction of new noble-gas molecules FNgBNR (Ng = Ar, Kr, and Xe; R = H, CH3, CCH, CHCH2, F, and OH).

We have computationally predicted a new class of stable noble-gas molecules FNgBNR (Ng = Ar, Kr, Xe; R = H, CH3, CCH, CHCH2, F, and OH). The FNgBNR were found to have compact structures with F-Ng bond lengths of 1.9-2.

Theoretical prediction on the thermal stability of cyclic ozone and strong oxygen tunneling.

Dual-level dynamics calculation with variational transition state theory including multidimensional tunneling has been performed on the isomerization reaction of cyclic ozone → normal (open) ozone, which was believed to be the stability-determining reaction of the elusive cyclic ozone molecule under thermal condition. The high-level potential energy surface data were obtained from the calculation using the MRCISD+Q theory with the aug-cc-pVQZ basis set, while the low-level reaction path information was obtained using the hybrid density functional theory B3LYP with the cc-pVTZ basis set. The calculated results showed very significant tunneling effects below 300 K (a factor of ∼200 at 300 K and over 10(7) at 200 K).

Multicoefficient density functional theory (MC-DFT).

We have systematically tested the performance of several pure and hybrid versions of density functional methods on different types of molecular energies by combining energies calculated using more than one basis sets. Most hybrid functionals show important performance improvement as compared to methods using only a single basis set. The results suggest that, in many cases, scaling the basis set corrections is also important for density functional theory calculation.