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Carbohydrates play essential roles in a variety of biological processes that are dictated by their structures. However, characterization of carbohydrate structures remains extremely difficult and generally unsolved. In this work, a de novo mass spectrometry-based workflow was developed to isolate and structurally elucidate oligosaccharides to provide sequence, monosaccharide compositions, and glycosidic linkage positions. The approach employs liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based methods in a 3-dimensional concept: one high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-QTOF MS) analysis for oligosaccharide sequencing and two ultra high performance liquid chromatography-triple quadrupole mass spectrometry (UHPLC-QqQ MS) analyses on fractionated oligosaccharides to determine their monosaccharides and linkages compositions. The workflow was validated by applying the procedure to maltooligosaccharide standards. The approach was then used to determine the structures of oligosaccharides derived from polysaccharide standards and whole food products. The integrated LC-MS workflow will reveal the in-depth structures of oligosaccharides.

Bovine κ-caseinoglycomacropeptide (GMP) is a highly modified peptide from κ-casein produced during the cheese making process. The chemical nature of GMP makes analysis by traditional proteomic approaches difficult, as the peptide bears a strong net negative charge and a variety of post-translational modifications. In this work, we describe the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) for the top-down analysis of GMP. The method allows the simultaneous detection of different GMP forms that result from the combination of amino acid genetic variations and post-translational modifications, specifically phosphorylation and O-glycosylation. The different GMP forms were identified by high resolution mass spectrometry in both negative and positive mode and confirmation was achieved by tandem MS. The results showed the predominance of two genetic variants of GMP that occur as either mono- or bi-phosphorylated species. Additionally, these four forms can be modified with up to two O-glycans generally sialylated. The results demonstrate the presence of glycosylated, bi-phosphorylated forms of GMP never described before.

The Bioaerosol Mass Spectrometry (BAMS) system was developed for the real-time detection and identification of biological aerosols using laser desorption ionization. Greater differentiation of particle types is desired; consequently MALDI techniques are being investigated. The small sample size ( approximately 1 microm3), lack of substrate, and ability to simultaneously monitor both positive and negative ions provide a unique opportunity to gain new insight into the MALDI process. Several parameters known to influence MALDI molecular ion yield and formation are investigated here in the single particle phase. A comparative study of five matrices (2,6-dihydroxyacetophenone, 2,5-dihydroxybenzoic acid, alpha-cyano-4-hydroxycinnamic acid, ferulic acid, and sinapinic acid) with a single analyte (angiotensin I) is presented and reveals effects of matrix selection, matrix-to-analyte molar ratio, and aerosol particle diameter. The strongest analyte ion signal is found at a matrix-to-analyte molar ratio of 100:1. At this ratio, the matrices yielding the least and greatest analyte molecular ion formation are ferulic acid and alpha-cyano-4-hydroxycinnamic acid, respectively. Additionally, a significant positive correlation is found between aerodynamic particle diameter and analyte molecular ion yield for all matrices. SEM imaging of select aerosol particle types reveals interesting surface morphology and structure.

Gas-phase zwitterionic amino acids were formed in complexes of underivatized beta-cyclodextrin through reactions with a neutral base, n-propylamine. The reaction was performed in the analyzer cell of an electrospray ionization-Fourier transform mass spectrometer. Most of the natural amino acids were studied with three cyclodextrin hosts including alpha-, beta-, and gamma-cyclodextrin to understand better the structural features that lead to the stabilization of the zwitterionic complexes. Molecular dynamics calculations were performed to provide insight into the structural features of the complexes. The rate constants of the reactions were obtained through kinetic plots. Examination of both L- and D-enantiomers of the amino acid showed that the reaction was enantioselective. The reaction was then employed to analyze mixtures of Glu enantiomers naturally occurring in the bacteria Bacillus licheniformis.

Structural analysis of sulfated oligosaccharides from kappa-carrageenan of up to ten residues (MW >2 kDa) was successfully carried out by positive mode nano-ESI-FTICR-MS together with MS/MS using sustained off-resonance irradiation-collision induced dissociation (SORI-CID). Glycosidic bond cleavage reactions via the B- and Y-types of fragmentation were observed and enabled complete sequencing of the oligosaccharide samples. The positions of the labile sulfate substituents were observable using SORI-CID, enabling the determination of the sequence of the sulfated residues.

Bioearosol mass spectrometry (BAMS) analyzes single particles in real time from ambient air, placing strict demands on instrument sensitivity. Modeling of the BAMS reflectron time of flight (TOF) with SIMION revealed design limitations associated with ion transmission and instrument sensitivity at higher masses. Design and implementation of a BAMS linear TOF with electrostatic ion guide and delayed extraction capabilities has greatly increased the sensitivity and mass range relative to the reflectron design. Initial experimental assessment of the new instrument design revealed improved sensitivity at high masses as illustrated when using standard particles of cytochrome C (m/z approximately 12,000), from which the compound's monomer, dimer (m/z approximately 24,000) and trimer (m/z approximately 36,000) were readily detected.

Protonated complexes of amino acids and underivatized beta-cyclodextrin, produced by electrospray ionization and trapped in the Fourier transform mass spectrometer, undergo formation of ternary complexes when reacted with alkyl amine. Based on the reactivities of the protonated amino acid complexes with alkylamines, the reactivities of the corresponding amino acid esters, and partially derivatized beta-cyclodextrin hosts, we conclude that the ternary complexes are salt-bridge zwitterionic species composed of amino acid zwitterions and protonated alkylamine all interacting with the hydroxyl groups on the narrow rim of the cyclodextrin. Molecular modeling calculations and experimental results suggest that the interactions of the amino acids with the rims contribute greatly to the formation of the zwitterionic species.

Non-covalent inclusion complexes formed between amino acids and derivatized calix[6]arenes are observed in MALDI mass spectrometry. The methyl, ethyl, and propyl ester derivatives of calix[6]arene yielded amino acid complexes, while the smaller calix[4]arene analogs did not. Similarly the underivatized calix[6]arene and calix[4]arene did not produce complexes. Amino acid complexes were observed for nearly all 20 amino acids in time-of-flight (TOF) analysis. In Fourier transform mass spectrometry (FTMS) analysis, however, only the most basic amino acids arginine, histidine, and lysine formed stable adducts. The complexes were abundant under matrix-assisted laser desorption ionization (MALDI) conditions, which suggested favorable interactions between host and guest.

A long-range glycosyl transfer reaction was observed in the collision-induced dissociation Fourier transform (CID FT) mass spectra of benzylamine-labeled and 9-aminofluorene-labeled lacto-N-fucopentaose I (LNFP I) and lacto-N-difucohexaose I (LNDFH I). The transfer reaction was observed for the protonated molecules but not for the sodiated molecules. The long-range glycosyl transfer reaction involved preferentially one of the two L-fucose units in labeled LNDFH I. CID experiments with labeled LNFP I and labeled LNFP II determined the fucose with the greatest propensity for migration. Further experiments were performed to determine the final destination of the migrating fucose. Molecular modeling supported the experiments and reaction mechanisms are proposed.

9-Aminofluorene (9AmFL) was investigated as an oligosaccharide label. The label was amenable to high UV detectability but did not interfere with mass spectrometric analysis. The 9AmFL label has high molar absorptivity (epsilon = 1.4 x 10(4) L cm(-1) mol(-1) at lambda = 267 nm), is chemically stable, and adds easily in reductive amination to the aldehyde terminus of oligosaccharides. Various linear and branched oligosaccharides were labeled with 9AmFL and the products were purified by chromatography on porous graphitized carbon (PGC). The derivatization reaction gave excellent yields (>95%). Up to 100-fold increase in UV sensitivity at lambda = 206 nm, compared to the corresponding alditol, was observed. Mass spectra were recorded for the labeled compounds. In the presence of sodium dopant, series of Y- and B-fragments were observed. Protonation of the labeled compounds prior to mass spectrometric analysis resulted in simplified spectra (Y-fragments only) and allowed for complete sequence analysis. The retention of the positive charge at the label in the protonated species was consistent with the basicity of the amine. The smallest amount of labeled sugar to be detected by photo-diode array (PDA) was 5 pmol (lambda = 267 nm).

Exoglycosidase digestion in combination with the catalog-library approach (CLA) is used with matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS) to obtain the complete structure of oligosaccharides. The CLA is a collision-induced dissociation (CID)-based method used to determine the structure of O-linked neutral oligosaccharides. It provides both linkage and stereochemical information. Exoglycosidases are used to confirm independently the validity of the CLA. In some cases, the CLA provides structural information on all but a single residue. Exoglycosidase is used to refine these structures. In this way, exoglycosidase use is targeted employing only a small number of enzymes. Exoglycosidase arrays, which have been used with N-linked oligosaccharides, is avoided despite the larger variations in structures of O-linked species.

The validity of the "three-point interaction" model is examined in the guest exchange reaction involving complexes of cyclodextrins and amino acids. The amino acid guest is exchanged in the gas phase in the presence of a gaseous alkyl amine. The net reaction is proton transfer between the protonated amino acid and the alkyl amine. The amino acid is lost as a neutral species. This reaction is sensitive to the chirality of the amino acid. Several amino acids are examined as well as the respective methyl esters to determine the role of the three interacting groups (ammonium, carboxylic acid, and side chain) in enantioselectivity. We find that the three-point interaction model is indeed valid in the gas phase. Enantioselectivity is optimal when two points of attraction and one repulsion is present in the gas-phase complex. The results are supported by molecular modeling calculations. A mechanism for the exchange is proposed.

Gas-phase noncovalently bound complexes are probed by hydrogen/deuterium exchange. The complexes, composed of a protonated amino acid and a monosaccharide, are investigated to observe the effects of complexation on the rates of exchange. Rate constants are determined and compared for complexed and uncomplexed amino acids. The overall rate constant, which corresponds to exchange of a specific number of hydrogens, is deconvoluted to yield site-specific rate constants. Complexation of amino acids with saccharides significantly decreases the rate constants of the exchange. Results of molecular orbital calculations are provided to explain the decrease in the rates.

The gas-phase basicities of oligomers of alanine and valine have been determined by bracketing measurements in an external source Fourier transform mass spectrometer. The results are compared to the oligomers of glycine, which were reported in an earlier publication, to observe the effect of the alkyl group and the increasing gas-phase basicity of the monomer units on the rates of proton transfer reactions. Molecular orbital calculations were performed on protonated triglycine and trialanine to determine how the alkyl groups affect intramolecular interactions. The results show that a high degree of ordering of the carbonyl groups is present in the protonated species. The carbonyl groups in turn order the side chain alkyl groups and decrease the rates of proton transfer reactions in, for example, the oligomers of valine.

The gas-phase hydrogen/deuterium (HID) exchange kinetics of several protonated amino acids and dipeptides under a background pressure of CH3OD were determined in an external source Fourier transform mass spectrometer. H/D exchange reactions occur even when the gas-phase basicity of the compound is significantly larger (> 20 kcal/mol) than methanol. In addition; greater deuterium incorporation is observed for compounds that have multiple sites of similar basicities. A mechanism is proposed that involves a structurally specific intermediate with extensive interaction between the protonated compound and methanol.

Unimolecular metastable decomposition of cucyclodextrin cations is observed in a fast-atom bombardment Fourier transform mass spectrometry instrument. Cleavage reactions occur at the glycosidic bonds to produce oligomeric fragment ions. The first-order rate constant for the decay of the protonated parent was measured and found to be (4.2 ± 1.0) × 10(2)s(-1).