Epitope Ligand Binding Sites of Blood Group Oligosaccharides in Lectins Revealed by Pressure-Assisted Proteolytic Excision Affinity Mass Spectrometry

Affinity mass spectrometry using selective proteolytic excision and extraction combined with MALDI and ESI mass spectrometry has been applied to the identification of epitope binding sites of lactose, GalNac, and blood group oligosaccharides in two blood group-specific lectins, human galectin-3 and glycine max lectin. The epitope peptides identified comprise all essential amino acids involved in carbohydrate recognition, in complete agreement with available X-ray structures. Tryptic and chymotryptic digestion of lectins for proteolytic extraction/excision-MS was substantially improved by pressure-enhanced digestion using an automated Barocycler procedure (40 kpsi). Both previously established immobilization on affinity microcolumns using divinyl sulfone and coupling of a specific peptide glycoprobe to the gold surface of a biosensor chip were successfully employed for proteolytic excision and extraction of carbohydrate epitopes and affinity measurements. The identified epitope peptides could be differentiated according to the carbohydrate employed, thus demonstrating the specificity of the mass spectrometric approach. The specificities of the epitope ligands for individual carbohydrates were further ascertained by affinity studies using synthetic peptide ligands with immobilized carbohydrates. Binding affinities of the synthetic ligand peptides to lactose, in comparison to the intact full-length lectins, were determined by surface acoustic wave (SAW) biosensor analysis and provided micromolar K_D values for the intact lectins, in agreement with results of previous ITC and SPR studies. Binding affinities of the epitope peptides were approximately two orders of magnitude lower, consistent with their smaller size and assembled arrangement in the carbohydrate recognition domains.

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Screening Anti-Cancer Drugs against Tubulin using Catch-and-Release Electrospray Ionization Mass Spectrometry

Tubulin, which is the building block of microtubules, plays an important role in cell division. This critical role makes tubulin an attractive target for the development of chemotherapeutic drugs to treat cancer. Currently, there is no general binding assay for tubulin–drug interactions. The present work describes the application of the catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay to investigate the binding of colchicinoid drugs to αβ-tubulin dimers extracted from porcine brain. Proof-of-concept experiments using positive (ligands with known affinities) and negative (non-binders) controls were performed to establish the reliability of the assay. The assay was then used to screen a library of seven colchicinoid analogues to test their binding to tubulin and to rank their affinities.

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Simple Approach for De Novo Structural Identification of Mannose Trisaccharides

Oligosaccharides have diverse functions in biological systems. However, the structural determination of oligosaccharides remains difficult and has created a bottleneck in carbohydrate research. In this study, a new approach for the de novo structural determination of underivatized oligosaccharides is demonstrated. A low-energy collision-induced dissociation (CID) of sodium ion adducts was used to facilitate the cleavage of desired chemical bonds during the dissociation. The selection of fragments for the subsequent CID was guided using a procedure that we built from the understanding of the saccharide dissociation mechanism. The linkages, anomeric configurations, and branch locations of oligosaccharides were determined by comparing the CID spectra of oligosaccharide with the fragmentation patterns based on the dissociation mechanism and our specially prepared disaccharide CID spectrum database. The usefulness of this method was demonstrated to determine the structures of several mannose trisaccharides. This method can also be applied in the structural determination of oligosaccharides larger than trisaccharides and containing hexose other than mannose if authentic standards are available.

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Screening Carbohydrate Libraries for Protein Interactions Using the Direct ESI-MS Assay. Applications to Libraries of Unknown Concentration

A semiquantitative electrospray ionization mass spectrometry (ESI-MS) binding assay suitable for analyzing mixtures of oligosaccharides, at unknown concentrations, for interactions with target proteins is described. The assay relies on the differences in the ratio of the relative abundances of the ligand-bound and free protein ions measured by ESI-MS at two or more initial protein concentrations to distinguish low affinity (≤10³ M^–1) ligands from moderate and high affinity (>10⁵ M^–1) ligands present in the library and to rank their affinities. Control experiments were performed on solutions of a single chain antibody and a mixture of synthetic oligosaccharides, with known affinities, in the absence and presence of a 40-component carbohydrate library to demonstrate the implementation and reliability of the assay. The application of the assay for screening natural libraries of carbohydrates against proteins is also demonstrated using mixtures of human milk oligosaccharides, isolated from breast milk, and fragments of a bacterial toxin and human galectin 3. Graphical Abstract

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Structural Analysis of Triacylglycerols by Using a MALDI-TOF/TOF System with Monoisotopic Precursor Selection

A new MALDI-TOF/TOF system with monoisotopic precursor selection was applied to the analysis of triacylglycerols in an olive oil sample. Monoisotopic precursor selection made it possible to obtain product-ion mass spectra without interference from species that differed by a single double bond. Complete structure determination of all triacylglycerols, including structural isomers, was made possible by interpreting the charge-remote fragmentation resulting from high-energy collision-induced dissociation (CID) of the sodiated triacylglycerols.      

Single-Photon Ionization of Organic Molecules Beyond 10 kDa

The volatilization and soft ionization of complex neutral macromolecules at low energies has remained an outstanding challenge for several decades [1]. Most volatilization techniques in mass spectrometry produce ions already in the source and most of them lead to particle velocities in excess of several hundred meters per second. For many macromolecules, post-ionization is inefficient since electronic or optical excitations can be followed by competing non-ionizing internal conversion, electron recapture, or fragmentation processes. Here, we explore the laser-assisted volatilization of neutral perfluoroalkyl-functionalized tetraphenylporphyrins as well as their single-photon ionization using vacuum ultraviolet (VUV) light at 157 nm. A systematic investigation of the ionization curves allows us to determine the molecular velocity distribution and ionization cross sections. We demonstrate the detection of single photon ionized intact organic molecules in excess of 10 kDa from a slow molecular beam.      

Gas-Phase Fragmentation of Oligoproline Peptide Ions Lacking Easily Mobilizable Protons

The fragmentation of peptides containing quaternary ammonium group, but lacking easily mobilizable protons, was examined with the aid of deuterium-labeled analogs and quantum-chemical modeling. The fragmentation of oligoproline containing quaternary ammonium group involves the mobilization of hydrogens localized at α- and γ- or δ-carbon atoms in the pyrrolidine ring of proline. The study of the dissociation pattern highlights the unusual proline residue behavior during MS/MS experiments of peptides.      

Overtone Mobility Spectrometry: Part 5. Simulations and Analytical Expressions Describing Overtone Limits

Mathematical expressions for the analytical duty cycle associated with different overtones in overtone mobility spectrometry are derived from the widths of the transmitted packets of ions under different instrumental operating conditions. Support for these derivations is provided through ion trajectory simulations. The outcome of the theory and simulations indicates that under all operating conditions there exists a limit or maximum observable overtone that will result in ion transmission. Implications of these findings on experimental design are discussed.      

Study of the Gas-Phase Intramolecular Aryltrifluoromethylation of Phenyl(Trifluoromethyl)Iodonium by ESI-MS/MS

The gas-phase reactions of the reactive λ ³-phenyl(trifluoromethyl)iodonium (PhI⁺(III)CF₃, 1 at m/z 273) to the radical cation of iodobenzene (PhI^?+, 2 at m/z 204) via the loss of ·CF₃ and the radical cation of trifluoromethylbenzene (PhCF₃ ^?+, 3 at m/z 146) via the loss of ·I, were studied by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Interestingly, the gas-phase intramolecular coupling reaction of CF₃ with phenyl via the CF₃ migration process of 1 at m/z 273 from iodine to the phenyl to give 3 at m/z 146 could only occur according to an intramolecular aromatic substitution mechanism. Density functional theory (DFT) calculations showed that the gas-phase intramolecular aryltrifluoromethylation of 1 at m/z 273 to 3 at m/z 146 occurred via a Meisenheimer complex intermediate (MC), where the triplevalent I center of 1 was reduced to monovalent I. Most importantly, the structure of 3 at m/z 146 derived from 1 at m/z 273 in ESI-MS/MS process was confirmed by comparison of its MS/MS with that of an authentic PhCF₃ ^?+ at m/z 146 acquired from the electron ionization (EI)-MS/MS analysis of PhCF₃. Thus, our studies revealed the intrinsic reactivity tendencies of λ³-phenyl(trifluoromethyl)iodonium under solvent-free conditions.      

Critical Evaluation of Kinetic Method Measurements: Possible Origins of Nonlinear Effects

The kinetic method is a widely used approach for the determination of thermochemical data such as proton affinities (PA) and gas-phase acidities (ΔH° _acid ). These data are easily obtained from decompositions of noncovalent heterodimers if care is taken in the choice of the method, references used, and experimental conditions. Previously, several papers have focused on theoretical considerations concerning the nature of the references. Few investigations have been devoted to conditions required to validate the quality of the experimental results. In the present work, we are interested in rationalizing the origin of nonlinear effects that can be obtained with the kinetic method. It is shown that such deviations result from intrinsic properties of the systems investigated but can also be enhanced by artifacts resulting from experimental issues. Overall, it is shown that orthogonal distance regression (ODR) analysis of kinetic method data provides the optimum way of acquiring accurate thermodynamic information.      

Decoding Split and Pool Combinatorial Libraries with Electron-Transfer Dissociation Tandem Mass Spectrometry

Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening “hit” are essential. Here we describe an electron-transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described “chiral oligomers of pentenoic amides (COPAs)” yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated ⁷⁹Br/⁸¹Br isotope “tags” to differentiate N- and C-terminal product ions. In addition, we have created “Hit-Find,” a software program that allows users to generate libraries in silico. The user can then search all possible members of the chemical library for those that fall within a user-defined mass error.      

Compatibility of Spatially Coded Apertures with a Miniature Mattauch-Herzog Mass Spectrograph

In order to minimize losses in signal intensity often present in mass spectrometry miniaturization efforts, we recently applied the principles of spatially coded apertures to magnetic sector mass spectrometry, thereby achieving increases in signal intensity of greater than 10× with no loss in mass resolution Chen et al. (J. Am. Soc. Mass Spectrom. 26, 1633–1640, 2015), Russell et al. (J. Am. Soc. Mass Spectrom. 26, 248–256, 2015). In this work, we simulate theoretical compatibility and demonstrate preliminary experimental compatibility of the Mattauch-Herzog mass spectrograph geometry with spatial coding. For the simulation-based theoretical assessment, COMSOL Multiphysics finite element solvers were used to simulate electric and magnetic fields, and a custom particle tracing routine was written in C# that allowed for calculations of more than 15 million particle trajectory time steps per second. Preliminary experimental results demonstrating compatibility of spatial coding with the Mattauch-Herzog geometry were obtained using a commercial miniature mass spectrograph from OI Analytical/Xylem.

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Biomimetic Antireflective Silicon Nanocones Array for Small Molecules Analysis

Biomimetic antireflective silicon nanocones array is used for analysis of small molecules by mass spectrometry. The role of the absorbed laser energy and its distribution in the laser desorption/ionization process has been investigated by varying the antireflective features precisely. By optimizing the antireflective silicon array, the absorbed laser energy can be channeled completely into the desorption/ionization of analytes. The optimized silicon array exhibits excellent performance to detect peptide, amino acid, drug molecule, and carbohydrate without any interference in the low-mass region.      

Liquid Injection Field Desorption Ionization Mass Spectrometry of Cyclic Metal Carbonyl Complexes with Tetra-Antimony Ligands

Reactions of (norbornadiene)Cr(CO)₄ or cis-(piperidine)₂Mo(CO)₄ with R₂Sb-SbR₂, and cyclo-(R′Sb)_n (R′ = Et, n-Pr; n = 4, 5) give the complexes cyclo-[M(CO)₄(R₂Sb-SbR′- SbR′-SbR₂)] (1: M = Cr, R = Me, R′= Et; 2: M = Mo, R = Et, R′ = Et; 3: M = Mo, R = Et, R′ = n-Pr). Not accessible to established characterization methods, the oily, extremely reactive unpurified mixture of 3 with scrambled ligands was characterized by mass spectrometry using liquid injection field desorption ionization (LIFDI).      

Dual-Channel Electrospray Microchip

A dual-channel electrospray microchip has been developed for electrospray ionization mass spectrometry (ESI-MS) where aqueous samples are mixed at the Taylor cone with an organic buffer. Due to the fast and effective mixing in the Taylor cone, the aqueous sample can be well ionized with a high ion intensity. The influence of geometric parameters such as the distance between the two microchannels at their junction at the tip of the emitter has been investigated together with chemical parameters such as the organic buffer composition.      

Negative Electron Transfer Dissociation Sequencing of 3-<Emphasis Type="Italic">O</Emphasis>-Sulfation-Containing Heparan Sulfate Oligosaccharides

Among dissociation methods, negative electron transfer dissociation (NETD) has been proven the most useful for glycosaminoglycan (GAG) sequencing because it produces informative fragmentation, a low degree of sulfate losses, high sensitivity, and translatability to multiple instrument types. The challenge, however, is to distinguish positional sulfation. In particular, NETD has been reported to fail to differentiate 4-O- versus 6-O-sulfation in chondroitin sulfate decasaccharide. This raised the concern of whether NETD is able to differentiate the rare 3-O-sulfation from predominant 6-O-sulfation in heparan sulfate (HS) oligosaccharides. Here, we report that NETD generates highly informative spectra that differentiate sites of O-sulfation on glucosamine residues, enabling structural characterizations of synthetic HS isomers containing 3-O-sulfation. Further, lyase-resistant 3-O-sulfated tetrasaccharides from natural sources were successfully sequenced. Notably, for all of the oligosaccharides in this study, the successful sequencing is based on NETD tandem mass spectra of commonly observed deprotonated precursor ions without derivatization or metal cation adduction, simplifying the experimental workflow and data interpretation. These results demonstrate the potential of NETD as a sensitive analytical tool for detailed, high-throughput structural analysis of highly sulfated GAGs.

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Resolution-Enhanced Kendrick Mass Defect Analysis of Polycyclic Aromatic Hydrocarbons and Fullerenes in the Diffusion Flame from a Butane Torch

A modified Kendrick Mass Defect (KMD) analysis was applied to the analysis of polycyclic aromatic hydrocarbons (PAHs) and fullerenes in the diffusion flame from a handheld butane torch.

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Carbonation and Other Super Saturated Gases as Solution Modifiers for Improved Sensitivity in Solvent Assisted Ionization Inlet (SAII) and ESI

Solvent Assisted Ionization Inlet (SAII) produces ions in a heated inlet to a mass spectrometer from aqueous and aqueous/organic solutions with high sensitivity. However, the use of acid modifiers, which typically aids electrospray ionization, generally results in ion suppression in SAII. Here we demonstrate that the use of carbonation and other super-saturated gases as solution modifiers increases analyte ion abundance and reduces metal cation adduction in SAII. Carbonation is also found to enhance electrospray ionization. The mechanistic and practical utility of carbonation in mass spectrometry is addressed.      

The sTOF,a Favorable Geometry for a Time-of-Flight Analyzer

A new geometry for the flight region in a time-of-flight mass spectrometer is presented. It consists of two opposing electrostatic sectors of about 255° each and straight sections with a length appropriate to the turns. The resulting geometry folds into a compact space. The first-order aberrations for position, angle, and energy are all zero. The transverse focusing properties are also excellent. For an energetic, high-divergence ion source such as laser ablation, the sTOF has higher resolution and ion transmission than a reflectron of similar physical size.

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