The mechanisms of collisional activation of ions in mass spectrometry

Suppression of Collision-Induced Dissociation in a Supersonically Expanding Gas

In high-resolution mass spectrometry, an electrospray ionization source is often paired with an ion-funnel to enhance ion transmission. Although it is established that ions experience collision-induced dissociation as they pass through this device, the impact of gas-flow dynamics on ion fragmentation remains unexplored. The present work demonstrates that the gas-flow dynamics from the capillary interface of an electrospray ionization source into an ion-funnel significantly reduces ion fragmentation. This reduction stems from the substantial decrease in the rate of increase in the internal energy of the ions, resulting from the collisions with a supersonically expanding gas. The results of this study have significant consequences for systems that employ electrospray mass spectrometry and ion-mobility spectrometry as well as in interdisciplinary fields involving ion transport through a gaseous medium.

Predicting Collision-Induced-Dissociation Tandem Mass Spectra (CID-MS/MS) Using Ab Initio Molecular Dynamics

Compound identification is at the center of metabolomics, usually by comparing experimental mass spectra against library spectra. However, most compounds are not commercially available to generate library spectra. Hence, for such compounds, MS/MS spectra need to be predicted. Machine learning and heuristic models have largely failed except for lipids. Here, quantum chemistry software can be used to predict mass spectra. However, quantum chemistry predictions for collision induced dissociation (CID) mass spectra in LC-MS/MS are rare. We present the CIDMD (Collision-Induced Dissociation via Molecular Dynamics) framework to model CID-based MS/MS spectra. It uses first-principles molecular dynamics (MD) to simulate the physical process of molecular collisions in CID tandem mass spectrometry. First, molecular ions are constructed at specific protonation sites. Using density functional theory, these protonated ions are targeted by argon collider gas atoms at user-specified velocities. Subsequent bond breakages are simulated over time for at least 1,000 fs. Each simulation is repeated multiple times from various collisional directions. Fragmentations are accumulated over those repeated collisions to generate CIDMD in silico mass spectra. Twelve small metabolites (<205 Da) were selected to test the accuracy of this framework in comparison to experimental MS/MS spectra. When testing different protomers, collider velocities, number of simulations, simulation time and impact factor b cutoffs, we yielded 261 predicted mass spectra. These in silico spectra resulted in entropy similarity scores of an average 624 ± 189 for all 261 spectra compared to their corresponding experimental spectra, which improved to 828 ± 77 when using optimal parameters of the most probable protomers for 12 molecules. With increasing molecular mass, higher velocities achieved better results. Similarly, different protomers showed large differences in fragmentation; hence, with increasing numbers of protomers and tautomers, the average CIDMD prediction accuracy decreased. Mechanistic details showed that specific fragment ions can be produced from different protomers via multiple fragmentation pathways. We propose that CIDMD is a suitable tool to predict mass spectra of small metabolites like produced by the gut microbiome.

Robustness of Threshold Collision-Induced Dissociation Simulations for Bond Dissociation Energies

The threshold collision-induced dissociation (T-CID) method is the workhorse for gas-phase bond dissociation energy (BDE) measurements. However, T-CID does not measure BDEs directly; instead, BDEs are obtained by fitting simulated data to the experimental data. We previously observed several large discrepancies between the computed and experimental BDEs. To analyze the reliability of the experimental values, we previously reported a study of the dissociation rate models in the simulation. Here, we report a study of the collision simulation part, specifically in the L-CID (ligand CID) program. We show that the BDE values are robust even to intentionally introduced mistakes in the simulations, varying in most cases by less than 3 kcal mol-1. The most significant exception is the collisional energy transfer (CET) simulation, which led to deviations larger than 10 kcal mol-1. However, we found that the BDEs obtained with explicitly simulated CET distributions deviated by only 3 kcal mol-1 from those simulated with the original model. Collectively, our results suggest that the T-CID-derived BDE values are robust and are likely to be accurate.

Discovery of Modified Metabolites, Secondary Metabolites, and Xenobiotics by Structure-Oriented LC-MS/MS

Exogenous compounds and metabolites derived from therapeutics, microbiota, or environmental exposures directly interact with endogenous metabolic pathways, influencing disease pathogenesis and modulating outcomes of clinical interventions. With few spectral library references, the identification of covalently modified biomolecules, secondary metabolites, and xenobiotics is a challenging task using global metabolomics profiling approaches. Numerous liquid chromatography-coupled mass spectrometry (LC-MS) small molecule analytical workflows have been developed to curate global profiling experiments for specific compound groups of interest. These workflows exploit shared structural moiety, functional groups, or elemental composition to discover novel and undescribed compounds through nontargeted small molecule discovery pipelines. This Review introduces the concept of structure-oriented LC-MS discovery methodology and aims to highlight common approaches employed for the detection and characterization of covalently modified biomolecules, secondary metabolites, and xenobiotics. These approaches represent a combination of instrument-dependent and computational techniques to rapidly curate global profiling experiments to detect putative ions of interest based on fragmentation patterns, predictable phase I or phase II metabolic transformations, or rare elemental composition. Application of these methods is explored for the detection and identification of novel and undescribed biomolecules relevant to the fields of toxicology, pharmacology, and drug discovery. Continued advances in these methods expand the capacity for selective compound discovery and characterization that promise remarkable insights into the molecular interactions of exogenous chemicals with host biochemical pathways.

The Spontaneous Electron-Mediated Redox Processes on Sprayed Water Microdroplets

Water is considered as an inert environment for the dispersion of many chemical systems. However, by simply spraying bulk water into microsized droplets, the water microdroplets have been shown to possess a large plethora of unique properties, including the ability to accelerate chemical reactions by several orders of magnitude compared to the same reactions in bulk water, and/or to trigger spontaneous reactions that cannot occur in bulk water. A high electric field (∼10⁹ V/m) at the air-water interface of microdroplets has been postulated to be the probable cause of the unique chemistries. This high field can even oxidize electrons out of hydroxide ions or other closed-shell molecules dissolved in water, forming radicals and electrons. Subsequently, the electrons can trigger further reduction processes. In this Perspective, by showing a large number of such electron-mediated redox reactions, and by studying the kinetics of these reactions, we opine that the redox reactions on sprayed water microdroplets are essentially processes using electrons as the charge carriers. The potential impacts of the redox capability of microdroplets are also discussed in a larger context of synthetic chemistry and atmospheric chemistry.

Effects of Hydrogen/Deuterium Exchange on Protein Stability in Solution and in the Gas Phase

Mass spectrometry (MS)-based techniques are widely used for probing protein structure and dynamics in solution. H/D exchange (HDX)-MS is one of the most common approaches in this context. HDX is often considered to be a "benign" labeling method, in that it does not perturb protein behavior in solution. However, several studies have reported that D₂O pushes unfolding equilibria toward the native state. The origin, and even the existence of this protein stabilization remain controversial. Here we conducted thermal unfolding assays in solution to confirm that deuterated proteins in D₂O are more stable, with 2-4 K higher melting temperatures than unlabeled proteins in H₂O. Previous studies tentatively attributed this phenomenon to strengthened H-bonds after deuteration, an effect that may arise from the lower zero-point vibrational energy of the deuterated species. Specifically, it was proposed that strengthened water-water bonds (W···W) in D₂O lower the solubility of nonpolar side chains. The current work takes a broader view by noting that protein stability in solution also depends on water-protein (W···P) and protein-protein (P···P) H-bonds. To help unravel these contributions, we performed collision-induced unfolding (CIU) experiments on gaseous proteins generated by native electrospray ionization. CIU profiles of deuterated and unlabeled proteins were indistinguishable, implying that P···P contacts are insensitive to deuteration. Thus, protein stabilization in D₂O is attributable to solvent effects, rather than alterations of intraprotein H-bonds. Strengthening of W···W contacts represents one possible explanation, but the stabilizing effect of D₂O can also originate from weakened W···P bonds. Future work will be required to elucidate which of these two scenarios is correct, or if both contribute to protein stabilization in D₂O. In any case, the often-repeated adage that "D-bonds are more stable than H-bonds" does not apply to intramolecular contacts in native proteins.

193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI

MALDI imaging allows for the near-cellular profiling of proteoforms directly from microbial, plant, and mammalian samples. Despite detecting hundreds of proteoforms, identification of unknowns with only intact mass information remains a distinct challenge, even with high mass resolving power and mass accuracy. To this end, many supplementary methods have been used to create experimental databases for accurate mass matching, including bulk or spatially resolved bottom-up and/or top-down proteomics. Herein, we describe the application of 193 nm ultraviolet photodissociation (UVPD) for fragmentation of quadrupole isolated singly charged ubiquitin (m/z 8565) by MALDI-UVPD on a UHMR HF Orbitrap. This platform permitted the high-resolution accurate mass measurement of not just terminal fragments but also large internal fragments. The outlined workflow demonstrates the feasibility of top-down analyses of isolated MALDI protein ions and the potential toward more comprehensive characterization of proteoforms in MALDI imaging applications.

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Characterization of ionized lignin model compounds with α-O-4 linkages by positive- and negative-ion mode electrospray ionization tandem mass spectrometry based on collision-activated dissociation

RATIONALE

The biggest obstacle in the rational conversion of biomass into aromatic chemicals is the identification of unknown compounds in lignin degradation mixtures that are highly complex. As opposed to lignin degradation products with β-O-4 linkages, very little is known about the mass spectrometric analysis of lignin degradation products with α-O-4 linkages.

METHODS

Lignin model compounds with an α-O-4 and another linkage, as well as lignin model compounds with only β-O-4 linkages, were ionized by attachment of lithium or sodium cations under positive-ion mode electrospray ionization (ESI) or by deprotonation in negative-ion mode ESI in a linear quadrupole ion trap mass spectrometer. The ions were subjected to collision-activated dissociation in multiple-stage tandem mass spectrometry experiments to characterize their fragmentation patterns.

RESULTS

All studied compounds formed abundant sodium and lithium cation adducts in positive-ion mode ESI with no fragmentation. Model compounds with β-O-4 linkages displayed stable [M - H]^- ions in negative-ion mode ESI whereas compounds with α-O-4 linkages only showed fragment ions. CAD of the lithiated α-O-4 compounds provided more structural information than CAD of sodiated compounds. However, both sodiated and lithiated compounds with α-O-4 linkages showed losses of monomer units at the MS² stage, which is useful for sequencing of lignins with this type of linkage.

CONCLUSIONS

An ionization and sequencing method has been developed for lignin model compounds with α-O-4 linkages that spontaneously fragment upon ionization via (-)ESI.

Optical and mass spectral characterization of the electrospray ionization/corona discharge ionization interface

The interchange between electrospray ionization (ESI) and corona discharge ionization (CDI) with respect to applied bias on the needle is customarily placed at the point where light production begins at the tip of the needle. If a liquid sample is flowing through a needle that is observed to produce light, the ionization process is assumed to be harsher and the term coronaspray ionization has been coined to describe this hybrid ionization mechanism. In this work, the transition between ESI and CDI is investigated with respect to applied bias through optical and mass spectrometric measurements. As a function of applied bias potential, the optical signal at the tip of the needle was recorded simultaneously with the resultant ionization products. In this effort, the production of ions from an electrospray ionization needle has been demonstrated to produce light regardless of bias if ions are also formed. With this understanding, an ESI/CDI needle was designed to allow the bias to be temporarily pulsed over the 'onset' voltage necessary for ionization and the rise and decay of the optical signal was measured. Positive mode CDI onset to a stable discharge state within 0.05 ms, while positive ESI required 1.9 ms to reach a stable condition. In the negative mode, the stability of the ionization process was highly variable in both ESI and CDI modes, though CDI was generally faster to reach the stable mode of operation. When the resultant ions were investigated, the effect of increased bias on an ESI needle was found to be species-dependent. Recognizing that the range of compounds probed was limited, for those examined, it appears that stable, non-labile species may be investigated via ESI under extremely high biases while labile species demonstrate a narrow range of stable biases before significant fragmentation occurs.

Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation

Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)₂, (αβ)₃, and (αβ)₄] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.

TUTORIAL: ION ACTIVATION IN TANDEM MASS SPECTROMETRY USING ULTRA-HIGH RESOLUTION INSTRUMENTATION

Tandem mass spectrometry involves isolation of specific precursor ions and their subsequent excitation through collision-, photon-, or electron-mediated activation techniques in order to induce unimolecular dissociation leading to formation of fragment ions. These powerful ion activation techniques, typically used in between mass selection and mass analysis steps for structural elucidation, have not only found a wide variety of analytical applications in chemistry and biology, but they have also been used to study the fundamental properties of ions in the gas phase. In this tutorial paper, a brief overview is presented of the theories that have been used to describe the activation of ions and their subsequent unimolecular dissociation. Acronyms of the presented techniques include CID, PQD, HCD, SORI, SID, BIRD, IRMPD, UVPD, EPD, ECD, EDD, ETD, and EID. The fundamental principles of these techniques are discussed in the context of their implementation on ultra-high resolution tandem mass spectrometers. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Efficient Mass Spectrometric Dissection of Glycans via Gold Nanoparticle-Assisted in-Source Cation Adduction Dissociation

Structural identification of glycans is important but remains challenging, for which tandem mass spectrometry has evolved as an indispensable tool. However, it requires additional complex hardware and extra time for ion extraction. Herein, we report a straightforward approach called gold nanoparticles (AuNPs)-assisted in-source cation adduction dissociation (isCAD) for efficient mass spectrometry (MS) dissection of glycans. Although AuNPs have been employed as an inorganic matrix for MALDI MS, this is the first report of AuNP-induced fragmentation. In this approach, AuNPs were employed as an energy absorber for laser ionization as well as a trigger for fragmentation, while residual or deliberately added sodium ions acted as a cationizing agent. The addition of sodium ions induced intensive fragmentation, but the addition of protons suppressed the fragmentation, allowing for facile tuning of the degree of fragmentation. In addition, it was found that larger oligosaccharides and glycans were much easier to fragment as compared with their smaller counterparts, and the use of high-concentration AuNPs effectively suppressed the degree of fragmentation and thereby provided abundant molecular ions. Without any extra hardware and ion extraction, this approach provides a straightforward, cost-efficient and tunable fragmentation for efficient MS dissection of saccharides, including monosaccharides, oligosaccharides, and glycans. Thus, it opens new access to efficient MS dissection of glycans.

Structural Characterization of Acidic Compounds in Pyrolysis Liquids Using Collision-Induced Dissociation and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

In this study, a novel approach to characterize and identify acidic oil compounds utilizing the fragmentational behavior of their corresponding precursor ions is presented. Precursor ions of seven analyzed pyrolysis oils that were generated from pyrolysis educts of different origins and degrees of coalification were produced by electrospray ionization in the negative ion mode (ESI(-)). Following a fragmentation of all ions in the ion cloud by collision-induced dissociation (CID), the precursor and product ions were subsequently detected by ultrahigh resolving Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The ESI(-)-CID data sets were evaluated by applying either a targeted classification or untargeted clustering approach. In the case of the targeted classification, 10% of the ionized precursor ions of the analyzed pyrolysis liquid samples could be classified into one of 11 compound classes utilizing theoretical fragmentation pathways of these classes. In contrast, theoretical fragmentation pathways were not necessary for the untargeted clustering approach, making it the more transmittable method. Results from both approaches were verified by analyzing standard compounds of known structure. The analysis and data evaluation methods presented in this work can be used to characterize complex organic mixtures, such as pyrolysis oils, and their compounds in-depth on a structural level.

Characterization of polyalphaolefins using halogen anion attachment in atmospheric pressure photoionization coupled with ion mobility spectrometry-mass spectrometry

Polyalphaolefins are saturated alpha olefin oligomers efficiently ionized by APPI.

Mass spectrometric characterization of protein structures and protein complexes in condensed and gas phase

Proteins are essential for almost all physiological processes of life. They serve a myriad of functions which are as varied as their unique amino acid sequences and their corresponding three-dimensional structures. To fulfill their tasks, most proteins depend on stable physical associations, in the form of protein complexes that evolved between themselves and other proteins. In solution (condensed phase), proteins and/or protein complexes are in constant energy exchange with the surrounding solvent. Albeit methods to describe in-solution thermodynamic properties of proteins and of protein complexes are well established and broadly applied, they do not provide a broad enough access to life-science experimentalists to study all their proteins' properties at leisure. This leaves great desire to add novel methods to the analytical biochemist's toolbox. The development of electrospray ionization created the opportunity to characterize protein higher order structures and protein complexes rather elegantly by simultaneously lessening the need of sophisticated sample preparation steps. Electrospray mass spectrometry enabled us to translate proteins and protein complexes very efficiently into the gas phase under mild conditions, retaining both, intact protein complexes, and gross protein structures upon phase transition. Moreover, in the environment of the mass spectrometer (gas phase, in vacuo), analyte molecules are free of interactions with surrounding solvent molecules and, therefore, the energy of inter- and intramolecular forces can be studied independently from interference of the solvating environment. Provided that gas phase methods can give information which is relevant for understanding in-solution processes, gas phase protein structure studies and/or investigations on the characterization of protein complexes has rapidly gained more and more attention from the bioanalytical scientific community. Recent reports have shown that electrospray mass spectrometry provides direct access to six prime protein complex properties: stabilities, compositions, binding surfaces (epitopes), disassembly processes, stoichiometries, and thermodynamic parameters.

(-)ESI/CAD MSn Procedure for Sequencing Lignin Oligomers Based on a Study of Synthetic Model Compounds with β-O-4 and 5-5 Linkages

Seven synthesized G-lignin oligomer model compounds (ranging in size from dimers to an octamer) with 5-5 and/or β-O-4 linkages, and three synthesized S-lignin model compounds (a dimer, trimer, and tetramer) with β-O-4 linkages, were evaporated and deprotonated using negative-ion mode ESI in a linear quadrupole ion trap/Fourier transform ion cyclotron resonance mass spectrometer. The collision-activated dissociation (CAD) fragmentation patterns (obtained in MS² and MS³ experiments, respectively) for the negative ions were studied to develop a procedure for sequencing unknown lignin oligomers. On the basis of the observed fragmentation patterns, the measured elemental compositions of the most abundant fragment ions, and quantum chemical calculations, the most important reaction pathways and likely mechanisms were delineated. Many of these reactions occur via charge-remote fragmentation mechanisms. Deprotonated compounds with only β-O-4 linkages, or both 5-5 and β-O-4 linkages, showed major 1,2-eliminations of neutral compounds containing one, two, or three aromatic rings. The most likely mechanisms for these reactions are charge-remote Maccoll and retro-ene eliminations resulting in the cleavage of a β-O-4 linkage. Facile losses of H₂O and CH₂O were also observed for all deprotonated model compounds, which involve a previously published charge-driven mechanism. Characteristic "ion groups" and "key ions" were identified that, when combined with their CAD products (MS³ experiments), can be used to sequence unknown oligomers.

Electron Transfer Dissociation of All Ions at All Times, MSETD, in a Quadrupole Time-of-Flight (Q-ToF) Mass Spectrometer

Data-independent mass spectral acquisition is particularly powerful when combined with ultra-performance liquid chromatography (LC) that provides excellent separation of most components present in a given sample. Data-independent analysis (DIA) consists of alternating full MS scans and scans with fragmentation of all ions within a selected m/z range, providing precursor masses and structure information, respectively. Fragmentation spectra are acquired either by sequential isolation and fragmentation of sliding m/z ranges or fragmenting all ions entering the MS instrument with no ion isolation, termed broadband DIA. Previously, broadband DIA has only been possible using collision induced dissociation (CID). Here, we report the use of electron transfer dissociation (ETD) as the fragmentation technique in broadband DIA instead of traditional collision induced dissociation (CID) during MS^E. In this approach, which we refer to as MS^ETD, we implement the inherent benefits provided by ETD, such as discrimination of leucine and isoleucine, in a DIA setup. The combination of DIA analysis and ETD fragmentation with supplemental CID energy provides a powerful platform to obtain information on all precursors and their sequence from a single experiment. Graphical Abstract ᅟ.

A Fundamental Tandem Mass Spectrometry Study of the Collision-Activated Dissociation of Small Deprotonated Molecules Related to Lignin

The collision-activated fragmentation pathways and reaction mechanisms of 34 deprotonated model compounds representative of lignin degradation products were explored experimentally and computationally. The compounds were evaporated and ionized by using negative-ion mode electrospray ionization doped with NaOH to produce abundant deprotonated molecules. The ions were isolated and subjected to collision-activated dissociation (CAD). Their fragment ions were then isolated and also subjected to CAD. This was repeated until no further fragmentation was observed (up to MS⁶ ). This approach enabled the identification of characteristic reaction pathways and delineation of reasonable fragmentation mechanisms for deprotonated molecules containing various functional groups. The varying fragmentation patterns observed for different types of compounds allow for the identification of the functionalities in these compounds. This information was utilized to identify the presence of specific functionalities and their combinations in molecules in an organosolv lignin sample.

Collision-Induced Dissociation of Electrosprayed NaCl Clusters: Using Molecular Dynamics Simulations to Visualize Reaction Cascades in the Gas Phase

Infusion of NaCl solutions into an electrospray ionization (ESI) source produces [Na_(n+1)Cl _n ]⁺ and other gaseous clusters. The n = 4, 13, 22 magic number species have cuboid ground state structures and exhibit elevated abundance in ESI mass spectra. Relatively few details are known regarding the mechanisms whereby these clusters undergo collision-induced dissociation (CID). The current study examines to what extent molecular dynamics (MD) simulations can be used to garner insights into the sequence of events taking place during CID. Experiments on singly charged clusters reveal that the loss of small neutrals is the dominant fragmentation pathway. MD simulations indicate that the clusters undergo extensive structural fluctuations prior to decomposition. Consistent with the experimentally observed behavior, most of the simulated dissociation events culminate in ejection of small neutrals ([NaCl] _i , with i = 1, 2, 3). The MD data reveal that the prevalence of these dissociation channels is linked to the presence of short-lived intermediates where a relatively compact core structure carries a small [NaCl] _i protrusion. The latter can separate from the parent cluster via cleavage of a single Na-Cl contact. Fragmentation events of this type are kinetically favored over other dissociation channels that would require the quasi-simultaneous rupture of multiple electrostatic contacts. The CID behavior of NaCl cluster ions bears interesting analogies to that of collisionally activated protein complexes. Overall, it appears that MD simulations represent a valuable tool for deciphering the dissociation of noncovalently bound systems in the gas phase. Graphical Abstract ᅟ.

Modeling collision energy transfer in APCI/CID mass spectra of PAHs using thermal-like post-collision internal energy distributions

The internal energy transferred when projectile molecular ions of naphthalene collide with argon gas atoms was extracted from the APCI-CID (atmospheric-pressure chemical ionization collision-induced dissociation) mass spectra acquired as a function of collision energy. Ion abundances were calculated by microcanonical integration of the differential rate equations using the Rice-Ramsperger-Kassel-Marcus rate constants derived from a UB3LYP/6-311G+(3df,2p)//UB3LYP/6-31G(d) fragmentation mechanism and thermal-like vibrational energy distributions p_ME,T_char. The mean vibrational energy excess of the ions was characterized by the parameter T_char ("characteristic temperature"), determined by fitting the theoretical ion abundances to the experimental breakdown graph (a plot of relative abundances of the ions as a function of kinetic energy) of activated naphthalene ions. According to these results, the APCI ion source produces species below T_char = 1457 K, corresponding to 3.26 eV above the vibrational ground state. Subsequent collisions heat the ions up further, giving rise to a sigmoid curve of T_char as a function of E_com (center-of-mass-frame kinetic energy). The differential internal energy absorption per kinetic energy unit (dE_vib/dE_com) changes with E_com according to a symmetric bell-shaped function with a maximum at 6.38 ± 0.32 eV (corresponding to 6.51 ± 0.27 eV of vibrational energy excess), and a half-height full width of 6.30 ± 1.15 eV. This function imposes restrictions on the amount of energy that can be transferred by collisions, such that a maximum is reached as kinetic energy is increased. This behavior suggests that the collisional energy transfer exhibits a pronounced increase around some specific value of energy. Finally, the model is tested against the CID mass spectra of anthracene and pyrene ions and the corresponding results are discussed.

Characteristics of Ion Activation and Collision Induced Dissociation Using Digital Ion Trap Technology

Collision induced dissociation (CID) is one of the most established techniques for tandem mass spectrometry analysis. The CID of mass selected ion could be realized by ion resonance excitation with a digital rectangular waveform. The method is simple, and highly efficient CID result could be obtained by optimizing the experimental parameters, such as digital waveform voltage, frequency, and q value. In this work, the relationship between ion trapping waveform voltage and frequency at preselected q value, the relationship between waveform frequency and the q value at certain ion trapping voltage for optimum CID efficiency were investigated. Experiment results showed that the max CID efficiency of precursor reserpine ions can be obtained at different trapping waveform voltage and frequency when q and β are different. Based on systematic experimental analysis, the optimum experimental conditions for high CID efficiency can be calculated at any selected β or q. By using digital ion trap technology, the CID process and efficient fragmentation of parent ions can be realized by simply changing the trapping waveform amplitude, frequency, and the β values in the digital ion trap mass spectrometry. The technology and method are simple. It has potential use in ion trap mass spectrometry. Graphical Abstract ᅟ.

Manifesting Subtle Differences of Neutral Hydrophilic Guest Isomers in a Molecular Container by Phase Transfer

Achieving strong host-guest interactions between synthetic hosts and hydrophilic guests in solution is challenging because solvation effects overwhelm other effects. To resolve this issue, we transferred complexes of cucurbit[7]uril (CB[7]) and monosaccharides to the gas phase and report here their intrinsic host-guest chemistry in the absence of solvation effects. It was observed that effective host-guest interactions in the gas phase mediated by ammonium cations allow the differentiation of the monosaccharide isomers in complex with CB[7] upon vibrational excitation. The potential of the unique observation was extended to a quantitative supramolecular analytical method for the monosaccharide guests. The combination of host-guest chemistry and phase transfer presented in this study is an effective approach to overcome current limitations in supramolecular chemistry.

On the structural denaturation of biological analytes in trapped ion mobility spectrometry – mass spectrometry

Trapped ion mobility spectra recorded for ubiquitin are consistent with structures reported for the native state by NMR.

Engaging challenges in glycoproteomics: recent advances in MS-based glycopeptide analysis

The proteomic analysis of glycosylation is uniquely challenging. The numerous and varied biological roles of protein-linked glycans have fueled a tremendous demand for technologies that enable rapid, in-depth structural examination of glycosylated proteins in complex biological systems. In turn, this demand has driven many innovations in wide ranging fields of bioanalytical science. This review will summarize key developments in glycoprotein separation and enrichment, glycoprotein proteolysis strategies, glycopeptide separation and enrichment, the role of mass measurement accuracy in glycopeptide detection, glycopeptide ion dissociation methods for MS/MS, and informatic tools for glycoproteomic analysis. In aggregate, this selection of topics serves to encapsulate the present status of MS-based analytical technologies for engaging the challenges of glycoproteomic analysis.

The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N-H and O-H stretching region and computational methods

IRMPD spectroscopy and computational chemistry techniques have been used to determine that the proton- and sodium-bound dimers of proline exist as a mixture of a number of different structures. Simulated annealing computations were found to be helpful in determining the unique structures of the protonated and sodiated dimers, augmenting chemical intuition. The experimental and computational results are consistent with the proton-bound dimer of N-protonated proline bound to zwitterionic proline. There was no spectroscopic evidence in the 3200-3800 cm(-1) region for a canonical structure which is predicted to have a weak N-H stretch at about 3440 cm(-1). A well resolved band at 1733 cm(-1) from a previous spectroscopic study (DOI: 10.1021/ja068715a ) was reassigned from a high energy canonical isomer to the C=O stretch of a lower energy zwitterionic structure. This band is a free carboxylate C=O stretch where protonated proline is hydrogen bonded to the other carboxylate oxygen which is also involved in an intramolecular hydrogen bond. Fifteen structures of the sodium bound proline dimer were computed to be within 10 kJ mol(-1) of Gibbs energy and eight structures were within 5 kJ mol(-1). None of these structures can be ruled out based on the experimental IRMPD spectrum. They all have an N-H stretching band predicted in a position that agrees with the experimental spectrum. However, only structures where one of the proline monomers is in the canonical form and having a free O-H bond can produce the band at ∼3600 cm(-1).

Exclusive selectivity in the one-pot formation of C-C and C-Se bonds involving Ni-catalyzed alkyne hydroselenation: optimization of the synthetic procedure and a mechanistic study

A unique Ni-catalyzed transformation is reported for the one-pot highly selective synthesis of previously unknown monoseleno-substituted 1,3-dienes starting from easily available terminal alkynes and benzeneselenol. The combination of a readily available catalyst precursor, Ni(acac)2, and an appropriately tuned phosphine ligand, PPh2Cy, resulted in the exclusive assembly of the s-gauche diene skeleton via the selective formation of C-C and C-Se bonds. The unusual diene products were stable under regular experimental conditions, and the products maintained the s-gauche geometry both in the solid state and in solution, as confirmed by X-ray analysis and NMR spectroscopy. Thorough mechanistic studies using ESI-MS revealed the key Ni-containing species involved in the reaction.

Dissociation of the anthracene radical cation: a comparative look at iPEPICO and collision-induced dissociation mass spectrometry results

The dissociation of the anthracene radical cation has been studied using two different methods: imaging photoelectron photoion coincidence spectrometry (iPEPCO) and atmospheric pressure chemical ionization-collision induced dissociation mass spectrometry (APCI-CID). Four reactions were investigated: (R1) C14H10(+•) → C14H9(+) + H, (R2) C14H9(+) → C14H8(+•) + H, (R3) C14H10(+•) → C12H8(+•) + C2H2 and (R4) C14H10(+•) → C10H8(+•) + C4H2. An attempt was made to assign structures to each fragment ion, and although there is still room for debate whether for the C12H8(+•) fragment ion is a cyclobuta[b]naphthalene or a biphenylene cation, our modeling results and calculations appear to suggest the more likely structure is cyclobuta[b]naphthalene. The results from the iPEPICO fitting of the dissociation of ionized anthracene are E0 = 4.28 ± 0.30 eV (R1), 2.71 ± 0.20 eV (R2), and 4.20 ± 0.30 eV (average of reaction R3) whereas the Δ(‡)S values (in J K(-1) mol(-1)) are 12 ± 15 (R1), 0 ± 15 (R2), and either 7 ± 10 (using cyclobuta[b]naphthalene ion fragment in reaction R3) or 22 ± 10 (using the biphenylene ion fragment in reaction R3). Modeling of the APCI-CID breakdown diagrams required an estimate of the postcollision internal energy distribution, which was arbitrarily assumed to correspond to a Boltzmann distribution in this study. One goal of this work was to determine if this assumption yields satisfactory energetics in agreement with the more constrained and theoretically vetted iPEPICO results. In the end, it did, with the APCI-CID results being similar.

ECD of tyrosine phosphorylation in a triple quadrupole mass spectrometer with a radio-frequency-free electromagnetostatic cell

A radio frequency-free electromagnetostatic (EMS) cell devised for electron-capture dissociation (ECD) of ions has been retrofitted into the collision-induced dissociation (CID) section of a triple quadrupole mass spectrometer to enable recording of ECD product-ion mass spectra and simultaneous recording of ECD-CID product-ion mass spectra. This modified instrument can be used to produce easily interpretable ECD and ECD-CID product-ion mass spectra of tyrosine-phosphorylated peptides that cover over 50% of their respective amino-acid sequences and readily identify their respective sites of phosphorylation. ECD fragmentation of doubly protonated, tyrosine-phosphorylated peptides, which was difficult to observe with FT-ICR instruments, occurs efficiently in the EMS cell.

Multiported pulsed valve interface for a linear quadrupole ion trap mass spectrometer to enable rapid screening of multiple functional-group selective ion-molecule reactions

Ion-molecule reactions provide a powerful tool for structural elucidation of ionized pharmaceutical analytes in tandem mass spectrometry. However, all previous interfaces for the introduction of reagents for ion-molecule reactions have utilized a single reagent approach. In this study, a multiported pulsed valve system was designed and characterized for rapid introduction of three neutral reagents into a linear quadrupole ion trap. Additionally, automatic triggering was used to allow for the introduction of the reagents on a chromatographic time scale. This system enables automatic, high throughput screening of complex mixtures by using at least three different ion-molecule reactions. Further, rapid testing of new neutral reagents is also possible.

Resonance activation and collision-induced-dissociation of ions using rectangular wave dipolar potentials in a digital ion trap mass spectrometer

Collision-induced dissociation (CID) of ions by resonance activation in a quadrupole ion trap is usually accomplished by resonance exciting the ions to higher kinetic energy, whereby the high kinetic energy ions collide with a bath gas, such as helium or argon, inside the trap and dissociate to fragments. A new ion activation method using a well-defined rectangular wave dipolar potential formed by dividing down the trapping rectangular waveform is developed and examined herein. The mass-selected parent ions are resonance excited to high kinetic energies by simply changing the frequency of the rectangular wave dipolar potential and dissociation proceeds. A relationship between the ion mass and the activation waveform frequency is also identified and described. This highly efficient (CID) procedure can be realized by simply changing the waveform frequency of the dipolar potential, which could certainly simplify tandem mass spectrometry analysis methods.

Efficient Sustainable Tool for Monitoring Chemical Reactions and Structure Determination in Ionic Liquids by ESI-MS

An easy and convenient procedure is described for monitoring chemical reactions and characterization of compounds dissolved in ionic liquids using the well-known tandem mass spectrometry (MS/MS) technique. Generation of wastes was avoided by utilizing an easy procedure for analysis of ionic liquid systems without preliminary isolation and purification. The described procedure also decreased the risk of plausible contamination and damage of the ESI-MS hardware and increased sensitivity and accuracy of the measurements. ESI-MS detection in MS/MS mode was shown to be efficient in ionic liquids systems for structural and mechanistic studies, which are rather difficult otherwise. The developed ESI-MS/MS approach was applied to study samples corresponding to peptide systems in ionic liquids and to platform chemical directed biomass conversion in ionic liquids.

Energy dependence of HCD on peptide fragmentation: stepped collisional energy finds the sweet spot

An understanding of the process of peptide fragmentation and what parameters are best to obtain the most useful information is important. This is especially true for large-scale proteomics where data collection and data analysis are most often automated, and manual interpretation of spectra is rare because of the vast amounts of data generated. We show herein that collisional cell peptide fragmentation, in this case higher collisional dissociation (HCD) in the Q Exactive, is significantly affected by the normalized energy applied. Both peptide sequence and energy applied determine what ion fragments are observed. However, by applying a stepped normalized collisional energy scheme and combining ions from low, medium, and high collision energies, we are able to increase the diversity of fragmentation ions generated. Application of stepped collision energy to HEK293T lysate demonstrated a minimal effect on peptide and protein identification in a large-scale proteomics dataset, but improved phospho site localization through increased sequence coverage. Stepped HCD is also beneficial for tandem mass tagged (TMT) experiments, increasing intensity of TMT reporters used for quantitation without adversely effecting peptide identification.

Mapping protein-ligand interactions in the gas phase using a functional group replacement strategy. Comparison of CID and BIRD activation methods

Intermolecular interactions in the gaseous ions of two protein-ligand complexes, a single chain antibody (scFv) and its trisaccharide ligand (α-D-Galp-(1→2)-[α-D-Abep-(1→3)]-α-Manp-OCH3, L1) and streptavidin homotetramer (S4) and biotin (B), were investigated using a collision-induced dissociation (CID)-functional group replacement (FGR) strategy. CID was performed on protonated ions of a series of structurally related complexes based on the (scFv + L1) and (S4 + 4B) complexes, at the +10 and +13 charge states, respectively. Intermolecular interactions were identified from decreases in the collision energy required to dissociate 50% of the reactant ion (Ec50) upon modification of protein residues or ligand functional groups. For the (scFv + L1)(10+) ion, it was found that deoxygenation of L1 (at Gal C3 and C6 and Man C4 and C6) or mutation of His101 (to Ala) resulted in a decrease in Ec50 values. These results suggest that the four hydroxyl groups and His101 participate in intermolecular H-bonds. These findings agree with those obtained using the blackbody infrared radiative dissociation (BIRD)-FGR method. However, the CID-FGR method failed to reveal the relative strengths of the intermolecular interactions or establish Man C4 OH and His101 as an H-bond donor/acceptor pair. The CID-FGR method correctly identified Tyr43, but not Ser27, Trp79, and Trp120, as a stabilizing contact in the (S4 + 4B)(13+) ion. In fact, mutation of Trp79 and Trp120 led to an increase in the Ec50 value. Taken together, these results suggest that the CID-FGR method, as implemented here, does not represent a reliable approach for identifying interactions in the gaseous protein-ligand complexes.

Structural characterization of chlorophyll-a by high resolution tandem mass spectrometry

A high resolution Fourier transform ion cyclotron resonance (FTICR) mass spectrometer is used for characterizing the fragmentation of chlorophyll-a. Three tandem mass spectrometry (MS/MS) techniques, including electron-induced dissociation (EID), collisionally activated dissociation (CAD), and infrared mutiphoton dissociation (IRMPD) are applied to the singly protonated chlorophyll-a. Some previously unpublished fragments are identified unambiguously by utilizing high resolution and accurate mass value provided by the FTICR mass spectrometer. According to this research, the two long aliphatic side chains are shown to be the most labile parts, and favorable cleavage sites are proposed. Even though similar fragmentation patterns are generated by all three methods, there are much more abundant peaks in EID and IRMPD spectra. The similarities and differences are discussed in detail. Comparatively, cleavage leading to odd electron species and H(•) loss both seem more common in EID experiments. Extensive loss of small side groups (e.g., methyl and ethyl) next to the macrocyclic ring was observed. Coupling the high performance FTICR mass spectrometer with contemporary MS/MS techniques, especially IRMPD and EID, proved to be very promising for the structural characterization of chlorophyll, which is also suitable for the rapid and accurate structural investigation of other singly charged porphyrinic compounds.

Dipolar direct current driven collision-induced dissociation in a digital ceramic-based rectilinear ion trap mass spectrometer

A digital ion trap (DIT) and rectilinear ion trap (RIT) have been proven to be very useful technology in the past years. In this work, the digital ion trap technology was combined with the ceramic-based rectilinear ion trap (cRIT) system. The rectangular waveform was used for ion trapping. A dipolar excitation waveform which was formed by dividing down the trapping rectangular waveform was used for the ion ejection. We found that the high efficient collision-induced dissociation (CID) procedure could be obtained by simply manipulating the duty cycle of the dipole excitation waveform, and it could significantly simplify the tandem mass spectrometry analysis method and procedure with an ion trap, since the dipolar direct current (dc) voltage could be easily produced and applied to one of the pair of electrodes, which was fully controlled by the computer software and does not need any hardware modification.

Gas-phase dissociation of glycosylated peptide ions

Among the myriad of protein post-translational modifications (PTMs), glycosylation presents a singular analytical challenge. On account of the extraordinary diversity of protein-linked carbohydrates and the great complexity with which they decorate glycoproteins, the rigorous establishment of glycan-protein connectivity is often an arduous experimental venture. Consequently, elaborating the interplay between structures of oligosaccharides and functions of proteins they modify is usually not a straightforward task. A more mature biochemical appreciation of carbohydrates as PTMs will significantly hinge upon analytical advances in the field of glycoproteomics. Undoubtedly, the analysis of glycosylated peptides by tandem mass spectrometry (MS/MS) will play a pivotal role in this regard. The goal of this review is to summarize, from an analytical and tutorial perspective, the present state of knowledge regarding the dissociation of glycopeptide ions as accomplished by various MS/MS methods. In addition, this review will endeavor to harmonize some seemingly disparate findings to provide a more complete and broadly applicable description of glycopeptide ion fragmentation. A fuller understanding of the rich variety of glycopeptide dissociation behaviors will allow glycoproteomic researchers to maximize the information yielded by MS/MS experiments, while also paving the way to new innovations in MS-based glycoproteomics.

Enhanced electron transfer dissociation of peptides modified at C-terminus with fixed charges

The impact of the conversion of carboxylates in peptides to basic or fixed charge sites on the outcome of electron transfer dissociation (ETD) is evaluated with respect to ETD efficiency and the number of diagnostic sequence ions. Four reagents, including benzylamine (BA), 1-benzylpiperazine (BZP), carboxymethyl trimethylammonium chloride hydrazide (GT), and (2-aminoethyl)trimethylammonium chloride hydrochloride (AETMA), were used for the carboxylate derivatization, with the first two replacing the acidic carboxylate groups with basic functionalities and the latter two introducing fixed charge sites. The ETD efficiencies and Xcorr scores were compared for both nonderivatized and derivatized tryptic and Glu-C peptides from cytochrome c. Derivatization of the carboxylate increases the average charge states, the number of fragment ions, and the dissociation efficiencies of peptides, especially for the fixed charge reagent, AETMA.