Collision-induced Dissociation Research Articles

Can OPAH ions be a source of CO and HCO in the interstellar medium? Lessons learned from the unimolecular dissociation of dibenzofuran and dibenz[b,f]oxepin radical cations

Unlike polycyclic aromatic hydrocarbons (PAHs), which are recognized to be key players in interstellar and astrochemistry, less is known about the astrochemical relevance of oxygen-containing PAHs (OPAHs). Small O-containing molecules such as CO and HCO are ubiquitous in the interstellar medium and understanding how OPAHs may be a source for these critical small molecules is important. To this end, we have studied the unimolecular reactions of two ionized OPAHs, dibenzofuran (1+•) and dibenz[b,f]oxepin (2+•) with tandem mass spectrometry (collision-energy resolved dissociation) and imaging photoelectron photoion coincidence spectroscopy (iPEPICO). Collision-induced dissociation (CID) results show the competition between the loss of carbon monoxide (CO) and loss of 29 Da (either the formyl radical (HCO) or sequential H loss), with the latter being the dominant reaction. Rice–Ramsperger–Kassel–Marcus (RRKM) modeling of the iPEPICO data, on the other hand, is consistent with the loss of CO from the parent ion at the dissociative ionization onset, and, in the case of 2+•, sequential H-atom loss from this product. There is significant difference between the two structurally similar systems. In 1+•, dissociation requires around 4 eV of ion internal energy, while only 2.5 eV internal energy is required for 2+• to fragment. Calculations at the CAM-B3LYP/6–311++G(d,p) level of theory were used to examine the reaction pathways. For CO loss in 1+•, the reaction is initiated by a ring expansion followed by contraction of the central ring forming an ion–molecule complex between protonated cyclopenta[3,4]cyclobuta[1,2]benzene and CO. HCO loss is preceded by H migration to a bridging carbon vicinal to the oxygen atom and subsequent ring re-organization to form a low energy cyclopenta[c][1]benzopyran cation. This channel is higher enough in energy to preclude its participation near threshold, but not at higher internal energies reached in the CID experiment, which could therefore involve both sequential H loss and HCO loss. In 2+•, the reaction starts with an opening of the central O-containing ring, lowering the energy demand relative to 1+•.

Photochemical and Collision-Induced Cross-Linking in Stereochemically Distinct Scaffolds of Peptides and Nitrile Imines in Gas-Phase Ions.

Intramolecular cross-linking between peptides and nitrile-imine intermediates was studied in stereochemically distinct conjugates in which the reacting components were mounted on cis-1,2-cyclohexane and trans-1,4-cyclohexane scaffolds that we call 1,2-s-peptides and 1,4-s-peptides, respectively. The nitrile-imine intermediates were generated by N2 loss from 2,5-diaryltetrazole tags upon UV-photodissociation at 213 and 250 nm or by collision-induced dissociation, and further interrogated by CID and UVPD-MS3. Peptide fragment ion series originating from linear structures and macrocyclic cross-links were distinguished and used to quantify the cross-linking yields. The yields in MS2 varied between 27% for AAAG conjugates to 78% for GAAAK conjugates, depending on the peptide sequence. The CID-MS3 yields were in a 57-97% range, depending on the peptide sequence. Structures of 1,2-s-peptide and 1,4-s-peptide ions as well as several of their nitrile-imine intermediates and cross-links were investigated by high-resolution cyclic ion mobility in combination with Born-Oppenheimer molecular dynamics and density functional theory calculations. Matches between the experimental and calculated collision cross sections and ion relative Gibbs energies were used to assign peptide structures. Peptide conjugates C-terminated with Gly and Lys residues underwent cross-linking by the carboxyl group, as established by MS3 sequencing and corroborated by carboxyl blocking experiments that lowered the cross-linking yields. Peptide conjugates C-terminated with Arg also cross-linked via the side-chain guanidine group. A notable feature of the 1,4-s-peptide ions was the participation of low-energy twist-boat cyclohexane conformers that was enforced by strong hydrogen bonds between the peptide and nitrile imine.

Structural elucidation of 14-membered ring macrolide antibiotics using electrospray ionization tandem mass spectrometry and density functional theory calculations.

Macrolides are critical antibiotics featuring a macrocyclic lactone core with deoxy sugars. Understanding their gas-phase fragmentation is challenging but essential for improving structural elucidation in mass spectrometry, which has implications for drug discovery and development. We used electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS) combined with quantum chemical calculations to investigate the fragmentation pathways of erythromycin A and roxithromycin. This approach helps elucidate the preferred fragmentation routes influenced by protonation sites. Macrolides showed similar fragmentation patterns, including sequential losses of saccharide or amino sugar units and dehydration from the macrocycle core. Multiple competitive pathways were observed, influenced by protonation sites. Computational studies confirmed the most favorable protonation sites and their impact on fragmentation, providing insights into key diagnostic product ions. Subsequent fragments involved rearrangement pathways such as alkene formation and cleavages via remote hydrogen transfers and pericyclic reactions. Our integrated approach offers a comprehensive understanding of macrolide fragmentation, enhancing structural elucidation and potential applications in drug development. This study advances mass spectrometry analysis of macrolides, contributing to pharmaceutical research by integrating orthogonal annotation methods and fragmentation studies.

Integrating Epoxidation, High-Resolution Mass Spectrometry and Ultraviolet Spectroscopy to Unravel the Complex Profile of Boswellic Acids and Related Compounds in the Boswellia serrata Gum Resin Extract

The chemical characterization of natural products is often a complex task that demands powerful analytical techniques. Liquid chromatography with high-resolution tandem mass spectrometry (HRMS/MS) is often employed, yet it can face hard challenges when isomeric species are present, and reference standards are lacking. In such cases, the confidence level in compound identification can be significantly improved by the collection of orthogonal information on target analytes. In this work, 23 key compounds in Boswellia serrata extract (BSE), 12 of which correspond to boswellic acids (BAs) and 11 to triterpenoidic acid isomers, were identified by combining RPLC followed by serial UV and ESI(-)-FTMS and FTMS/MS detections with the evaluation of the reactivity towards C=C bond epoxidation with meta-chloroperoxybenzoic acid (m-CPBA), proposed as a fast chemical tool to gather information about C=C bond steric hindrance, a key structural feature of BAs and related compounds. The interpretation of UV spectra acquired after chromatographic separation corroborated the identification of the substitution patterns of enonic and dienic residues in ketoboswellic and dehydroboswellic acids. Moreover, MS/MS based on higher-energy collision-induced dissociation (HCD) unveiled new fragmentation pathways, providing important structural details on target analytes. The integrated approach developed during this study might pave the way for a deeper understanding of the BSE bioactive properties. Moreover, it can be considered an example of a more general strategy for the analysis of complex mixtures of natural compounds including also isomeric species.

Radical-directed dissociation mass spectrometry for differentiation and relative quantitation of isomeric ether-linked phosphatidylcholines

BackgroundEther-linked phosphatidylcholines (PCs) include both plasmanyl and plasmenyl PCs, which contain an ether or a vinyl ether bond at the sn-1 linkage position, respectively. Profiling and quantifying ether PCs with accurate structural information is challenging because of the common presence of isomeric and isobaric species in a lipidome. ResultsIn the present study, radical directed dissociation (RDD) from collision-induced dissociation (CID) of the bicarbonate anion adduct of ether PCs has been investigated to differentiate and relatively quantify ether PCs. Alkyl- and alkenyl- PCs give diagnostic characteristic fragment patterns that enable their confident identification and isomer differentiation. Additionally, the sn-position specific product ions have proven effective for relative quantitation among isomers in ether PCs and their isobaric PC species. Using this methodology, we successfully identified a total of 30 PC-O species, 21 PC-P species at the chain composition level, and 22 species of isobaric PC at the sn-position level in the human plasma lipid extract. The quantitative analysis revealed that ether PCs with a 20:4 fatty acyl chain are relatively more abundant in human plasma. Finally, the profile of ether PCs in type 2 diabetic (T2D) groups compared to normal control groups revealed a significant decrease in PC-O 18:1/20:5. We also found it is the PC species containing a 17-carbon fatty acyl chain, rather than their isobaric ether PCs, that shows a decreasing trend in the T2D groups. Significanceether-linked PCs are firstly investigated by RDD mass spectrometry.

Advances in Mass Spectrometry Fragmentation Techniques for Peptide and Protein Characterization: CID to ETD

Mass spectrometry (MS) has transformed the field of proteomics by enabling the precise analysis of proteins and peptides at the molecular level. The heart of this analysis is the process of fragmentation, which plays a pivotal role in elucidating amino acid sequence, identifying post-translational modifications (PTMs), and characterizing structural features. Peptides and proteins are first ionized and then subjected to fragmentation techniques such as Collision-Induced Dissociation (CID), Electron-Transfer Dissociation (ETD), and Electron-Capture Dissociation (ECD). These techniques induce fragmentation along the peptide backbone, generating characteristic fragment ions (b and y ions, c and z ions) that reflect the sequence of amino acids. The mass-to-charge (m/z) ratios of these fragment ions provide crucial data for de novo sequencing and PTM identification. Furthermore, fragmentation patterns can reveal insights into protein folding, interactions, and dynamics. This article provides the detailed view of mass fragmentation techniques in peptides and proteins, highlighting its importance in advancing proteomic research and its applications in fields ranging from biomarker discovery to drug development.

Conversion of 5α-Androstane-3α,17β-diol to bis[(4-dimethylamino)phenyl carbamate] derivative for sensitive determination of its rat brain level by LC/ESI-MS/MS.

5α-Androstane-3α,17β-diol (3α,5α-Adiol) is a testosterone-derived neurosteroid and has anxiolytic and analgesic effects via γ-aminobutyric acid type A receptors as with the progesterone-derived neurosteroid, allopregnanolone (AP). Although the psychotropic drug-evoked changes in the brain AP concentration have been intensively studied, those in the brain 3α,5α-Adiol concentration remain poorly understood. One of the causes for this is the limited availability of a validated method for quantifying the brain 3α,5α-Adiol with a sufficient sensitivity and specificity, which is described in this study. To enhance the detectability of 3α,5α-Adiol by electrospray ionization-tandem mass spectrometry (ESI-MS/MS), derivatization with 4-dimethylaminobenzoyl azide was employed. The brain sample was purified by solid-phase extraction and the recovered 3α,5α-Adiol and the deuterated internal standard were derivatized, then measured by liquid chromatography (LC)/ESI-MS/MS with selected reaction monitoring. The derivatized 3α,5α-Adiol, i.e., the bis[(4-dimethylamino)phenyl carbamate] derivative, provided the intense doubly-protonated molecule as the precursor ion, then the specific product ion containing the 3α,5α-Adiol-skeleton by collision-induced dissociation. The detectability of 3α,5α-Adiol was eventually increased 1000-fold by derivatization. Separation of the derivatized 3α,5α-Adiol from its stereoisomers and interfering brain components was achieved using a SunShell Biphenyl column with an isopropyl alcohol-containing mobile phase. A good linearity in the sufficient concentration range, acceptable precision and accuracy, and negligible matrix effect were demonstrated by the validation tests. The animal (rat) study using this method revealed that the brain 3α,5α-Adiol levels were unaffected by the administration of fluoxetine (FLX) and clozapine (CLZ), in contrast to the significant increase of the AP levels. An LC/ESI-MS/MS method capable of quantifying 3α,5α-Adiol in the rat brain using a 20-mg tissue was developed and validated. The brain levels of 3α,5α-Adiol had an entirely different behavior from those of AP due to FLX and CLZ administration.

Sensitive determination of volatile nitrosamines with ambient pressure ammonium-adduct ionization mass spectrometry.

In recent years, the control of volatile N-nitrosamines (NAs) has been of interest in the pharmaceutical and food industries, as many of these compounds are probable human carcinogens. Thus, rapid and trace-level quantitative determination methods are in urgent demand. In this work, ambient pressure ammonium-adduct ionization mass spectrometry was proposed for the sensitive detection of volatile nitrosamines in various pharmaceutical headspaces. The ammonium ions produced through electrospray ionization acted as reactant ions for NAs to generate ammonium-NA adduct ions and underwent in-source collision-induced dissociation to produce protonated NAs, which were detected by mass spectrometry. The ionization selectivity and sensitivity for various volatile NAs were improved significantly using the developed method, which was demonstrated by the limit of quantification (LOQ) below 52ng L-1 for all NAs, and the quantitative performance was consequently improved. Different NAs exhibited almost equimolar response using NH4+ as the reactant ion, with at least a twofold enhancement in intensity for the individual compounds relative to when using H+ as the reactant ion. The proposed method is a rapid, sensitive, and environmentally economical approach that uses few reagents.

Characterization of glycylglycyltyrosine radical cations: Insights into β-radical formation and N–Cα peptide bond dissociation at the tyrosine residue

We investigated the dissociation and characterization of radical cations of glycylglycyltyrosine [GGY]•+, focusing on β-radical-induced N–Cα peptide bond cleavage reactions at the tyrosyl residue. By combining density functional theory (DFT) calculations with experimental studies utilizing low-energy collision-induced dissociation (CID) mass spectrometry and deuterium labeling on the two β-hydrogen atoms of the tyrosyl residue in [GGY]•+, we elucidated the intricacies of the β-radical structure and its origin. Unlike tryptophan-containing [GGW]•+, which forms canonical π-radical precursors, infrared multiphoton dissociation (IRMPD) spectroscopy results reveal that the β-radical [GGYβ•]+ isomerizes from the phenoxy-radical [GGYo•]+, with the radical localized on the β-carbon of the tyrosyl residue and the phenolic oxygen atom, respectively. The isomerization barriers from [GGYo•]+ to [GGYβ•]+ are <109 kJ mol−1.

Influence of 5-fluorination on the structure and glycosidic bond stability of the protonated canonical DNA and RNA cytidine nucleosides: Oh, what a difference the 2′-hydroxy substituent makes?

Fluorinated nucleosides are well-established as anticancer and antiviral medications. As with many pharmaceuticals, the effects of fluorine modifications are often only partially understood. In this work, the effects of 5-fluorination of the cytosine nucleobase on the structures and glycosidic bond stabilities of the protonated canonical DNA and RNA cytidine nucleosides (dCyd and Cyd) are examined. Infrared multiple photon dissociation action spectroscopy experiments and electronic structure calculations are employed to probe the structural influences of 5-fluorination. Spectral signatures in the IR fingerprint and hydrogen-stretching regions indicate that 5-fluorination heavily directs for and solely produces O2 protonation para to the 5-fluoro substituent. This differs from the canonical cytidine nucleosides where roughly equal populations of O2 and N3 protonated structures were observed. Energy-resolved collision-induced dissociation experiments combined with survival yield analyses are performed to probe the influence of 5-fluorination on glycosidic bond stability. Trends in the energy-dependence of the survival yield curves indicate that 5-fluorination weakens the glycosidic bond, and that the influence of 5-fluorination on glycosidic bond stability is much greater for dCyd than Cyd. Theory also finds that 5-fluorination weakens the glycosidic bond but predicts that the influence of 5-fluorination on N-glycosidic bond stability is roughly the same for dCyd and Cyd. Oh, what a difference the 2′-hydroxy substituent makes?

B-166 Differentiation of Aziridine Functionality from Related Functional Groups in Protonated Analytes by Using Selective Ion-Molecule Reactions

Abstract Background The development of better methods for the rapid and reliable identification of unknown compounds in mixtures is urgently needed in drug development. Aziridines, in particular, are used for drug synthesis but are potentially mutagenic and carcinogenic compounds. However, the detection and identification of these compounds pose challenges for many analytical methods, such as Nuclear Magnetic Resonance (NMR) spectroscopy, Fourier-transform infrared spectroscopy (FT-IR), and X-ray crystallography. These techniques are time-consuming and often require large quantities of highly pure compounds. Methods Therefore, this study demonstrates that selective gas-phase ion-molecule reactions of protonated analytes with neutral tris(dimethylamino)borane (TDMAB), followed by diagnostic collision-activated dissociation (CAD), can be used to differentiate aziridines from structurally related compounds in a modified linear quadrupole ion trap (LQIT) mass spectrometer. The experiments were performed using an atmospheric pressure chemical ionization (APCI) source in positive ion detection mode. TDMAB was purchased from Sigma-Aldrich and used without purification. It was introduced into the ion trap (2 mtorr of helium buffer gas) via an external reagent mixing manifold through a syringe pump at a flow rate of 10 μL h-1 and diluted with helium before entering the ion trap through a variable leak valve. All analytes were prepared at a concentration of 1 mM in methanol. The protonated analytes were transferred into the ion trap, isolated, and allowed to react with TDMAB (MS2 experiments). Results Product ions formed upon reactions of the analyte ions with TDMAB were subjected to a collision-activated dissociation (CAD) experiment (MS3 experiments). CAD on product ions produced diagnostic fragment ions with 25- and 43 m/z-units lower m/z values than the adduct - DMA product ions. Quantum chemical calculations were employed using the Gaussian 16 program calculated at the M06-2X/6-311++G(d,p) level of theory to provide theoretical foundation and to explore the underlying mechanisms of the observed gas-phase reactions. None of the tested structurally related analytes produced a similar fragmentation pattern Conclusions The innovative approach presented in this study offers a promising avenue for enhancing efficiency and accuracy in drug development. The successful differentiation of aziridine is an alternative method in overcoming the limitation of traditional techniques. The findings from the research contributes to the advancement of analytical techniques, addressing critical issues in identifying impurities in drug products. The versatility of the methods extends beyond drug developments, making it applicable in various other fields such as in molecular diagnostics, metabolism and laboratory medicines.

B-182 Development and validation of an LC-MS/MS assay for simultaneous measurement of serum androstenedione and 17-hydroxyprogesterone in serum

Abstract Background Androstenedione and 17-hydroxyprogesterone are measured via immunoassays or high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS) in clinical laboratories. Immunoassays have limited sensitivity and specificity for certain steroid hormones testing. We aimed to develop and validate a sensitive, accurate, and specific in-house LC-MS/MS assay to simultaneously measure both 17-hydroxyprogesterone and androstenedione in serum. Methods 13C-labeled androstenedione and 17-hydroxyprogesterone internal standards were added to calibrator, control, and patient samples. A hexane/ethyl acetate solution was used in a liquid-liquid extraction procedure. The organic layer was then removed and dried followed by reconstituting the extracts in 2.5 mM ammonium formate in 50% methanol. The HPLC mobile phase gradient began with 47%, 2.5 mM ammonium formate in water and 53%, 2.5 mM ammonium formate in methanol. This progressed to 56% of the methanol phase over three minutes. The mixtures were separated though an Agilent 1260 Infinity HPLC system with a Poroshell 120 EC-C18 analytical column (2.1 × 50 mm × 2.7 µm). The separated HPLC eluents then entered an Agilent 6460C QQQ mass spectrometer in positive ion mode through an electrospray ionization source where protonated androstenedione (m/z = 287.2) with the protonated androstenedione-[2, 3, 4-13C3] internal standard (m/z = 290.2) and protonated 17-hydroxyprogesterone (m/z = 331.2) with the protonated 17-hydroxyprogesterone-[2, 3, 4-13C3] (m/z = 334.2) were mass-selected for collision-induced dissociation. For androstenedione, respective quantifier and qualifier m/z values of 287.2 &amp;gt; 97.1 and 287.2 &amp;gt; 109.1 were used while respective quantifier and qualifier m/z values of 331.2 &amp;gt; 97.1 and 331.2 &amp;gt; 109.1 were used for 17-hydroxyprogesterone. Validation studies were performed including imprecision, lower limit of quantitation (LLOQ), analytical measurement range (AMR), interference, specificity, carryover, extraction recovery, matrix effect, and comparison with a reference laboratory LC-MS/MS method. The total allowable error limits used in this study were 23.5% for androstenedione and 30.2% for 17-hydroxyprogesterone. Results Total imprecision results across three concentrations yielded a maximum CV of 4.6 % for androstenedione and 6.5% for 17-hydroxyprogesteron. The AMRs of androstenedione and 17-hydroxyprogesterone were 0.2 to 13.4 and 0.1 to 22.0 ng/mL without significant carryovers. No significant interferences were observed from 11-deoxycorticosterone (700 ng/dL), testosterone (2500 ng/dL), DHEA (1000 ng/mL), bilirubin (30.1 mg/dL), hemoglobin (1032 mg/dL), or triglycerides (1858 mg/dL). The extraction recoveries of androstenedione and 17-hydroxyprogesterone were 98% and 81%, respectively. No significant matrix effects were identified. In comparison to the reference lab LC-MS/MS method, the in-house LC-MS/MS assay demonstrated a 0.523% bias for androstenedione and a -3.77% bias for 17-hydroxyprogesterone with both exhibiting excellent correlations with the reference lab measurements. More specifically, our results (as a function of values obtained from the reference lab) followed the relationship of y = 1.039x - 0.092 (R = 0.9951) for androstenedione and y = 0.957x + 0.01 (R = 0.9974) for 17-hydroxyprogesterone. Conclusions An LC-MS/MS assay is developed for simultaneous detection of serum androstenedione and 17-hydroxyprogesterone. The assay demonstrates acceptable imprecision, AMR, and accuracy. No significant carryover and interference from other structurally similar steroid hormones and other common interferents are identified.

Recent additions and access to a multidimensional lipidomic database containing liquid chromatography, ion mobility spectrometry, and tandem mass spectrometry information.

The importance of lipids in biology continues to grow with their recent linkages to more diseases and conditions, microbiome fluctuations, and environmental exposures. These associations have motivated researchers to evaluate lipidomic changes in numerous matrices and studies. Lipidomic analyses, however, present numerous challenges as lipid species have broad chemistries that require different extraction methods and instrumental analyses to evaluate and separate their many isomers and isobars. Increasing knowledge about different lipid characteristics is therefore crucial for improving their separation and identification. Here, we present a multidimensional database for lipids analyzed on a platform combining reversed-phase liquid chromatography, drift tube ion mobility spectrometry, collision-induced dissociation, and mass spectrometry (RPLC-DTIMS-CID-MS). This platform and the different separation characteristics it provides enables more confident lipid annotations when compared to traditional tandem mass spectrometry platforms, especially when analyzing highly isomeric molecules such as lipids. This database expands on our previous publication containing only human plasma and bronchoalveolar lavage fluid lipids and provides experimental RPLC retention times, IMS collision cross section (CCS) values, and m/z information for 877 unique lipids from additional biofluids and tissues. Specifically, the database contains 1504 precursor [M + H]+, [M + NH4]+, [M + Na]+, [M-H]-, [M-2H]2-, [M + HCOO]-, and [M + CH3COO]- ion species and their associated CID fragments which are commonly targeted in clinical and environmental studies, in addition to being present in the chloroform layer of Folch extractions. Furthermore, this multidimensional RPLC-DTIMS-CID-MS database spans 5 lipid categories (fatty acids, sterols, sphingolipids, glycerolipids, and glycerophospholipids) and 24 lipid classes. We have also created a webpage (tarheels.live/bakerlab/databases/) to enhance the accessibility of this resource which will be populated regularly with new lipids as we identify additional species and integrate novel standards.

Rapid on-site detection of illicit drugs in urine using C18 pipette-tip based solid-phase extraction coupled with a miniaturized mass spectrometer

Drug abuse is a social issue worldwide, and there is an increasing demand for on-site rapid detection of illicit drugs. In this study, a rapid and simple analytical method for the detection of 6-monoacetylmorphine (6-MAM), methamphetamine (MA), methylenedioxymethamphetamine (MDMA), ketamine (K), norketamine (NK), and cocaine (COC) in urine was developed. The developed method combines C18 pipette-tip based solid-phase extraction (C18 PT-SPE) with a miniaturized mass spectrometer (miniMS), exhibiting remarkable simplicity, high sensitivity, and strong reliability, compared with the conventional method. The optimal extraction and elution conditions for C18 PT-SPE were considered as 9 and 3 aspirating-dispensing cycles, respectively. The miniMS parameters including spray voltage, isolation potential, and collision-induced dissociation energy for the detection of these six illicit drugs were optimized using a nano-electrospray ionization method. The limit of detection (LOD), limit of quantification (LOQ), linear range, and linearity for the analysis of six illicit drugs in urine with the proposed C18 PT-SPE-miniMS method were determined. Except for the LOD of K and COC was determined as 0.5 and 0.25 ng mL−1 respectively, and the LOD of 6-MAM MA, MDMA, and NK was determined as 1 ng mL−1. This method enables rapid on-site detection, providing easier operation, lower cost, and better portability compared to conventional methods, making it a potential tool in drug crime investigation and forensic science.

Structural characterization and bioactivity profiling of the fungal peptaibiotic tolypin reveal protective effects against influenza viruses.

In a bioprospection for new antivirals, we tested nonribosomally biosynthesized polypeptide antibiotics in MDCK II cells for their actions on influenza A and B viruses (IAV/IBV). Only tolypin, a mixture of closely related 16-residue peptaibiotics from the fungus Tolypocladium inflatum IE 1897, showed promising activity. It was selected for further investigation and structural characterization byultrahigh performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HR-MS/MS) and ultrahigh performance liquid chromatography coupled to in-source collision-induced dissociation tandem mass spectrometry (UHPLC-isCID-HR-MS/MS), revealing 12 partially co-eluting individual peptides that were fully sequenced. Since tolypin-related efrapeptins are potent inhibitors of F1/Fo-ATPase, we screened tolypin for its toxicity against MDCK II cells and larvae of the greater wax moth Galleria mellonella. We found that a nontoxic concentration of tolypin (1 µg/mL) reduced the titer of two IBV strains by 4-5 log values, and that of an H3N2 strain by 1-2 log values, but the H1N1pdm strain was not affected. The higher concentrations of tolypin were cytostatic to MDCK II cells, shifted their metabolism from oxidative phosphorylation to glycolysis, and induced paralysis in G. mellonella, supporting the inhibition of F1/Fo-ATPase as the mode of action. Our results lay the foundations for future work to investigate the interplay between viral replication and cellular energy metabolism, as well as the development of drugs that target host factors.

Derivatization of Undecahalogenated closo-Dodecaborates [B12X11NH3]- (X = F-I): Attaching Isocyanate, Amidinium, and Formamide Functionalities.

Halogenated closo-dodecaborates are very robust and versatile weakly coordinating anions for numerous applications. The introduction of additional substituents, e.g., pseudohalides, allows the tuning of their chemical and physical properties. In this report, the synthesis of the isocyanate-substituted closo-dodecaborates [B12X11(NCO)]2- (X = H, F-I) was investigated. In an attempt to synthesize the undecahalogenated derivatives, a selective and halogen-dependent reaction yielding boron clusters carrying the functional groups amidinium (-NHCHNMe2) and formamide (-NHC(O)H) was discovered. The halogenated anions were fully characterized by vibrational and NMR spectroscopy, mass spectrometry, and X-ray diffraction. Salts of the formamide-substituted anion [B12X11(NHC(O)H)]2- are surprisingly thermally stable in the condensed phase. In contrast, collision-induced dissociation in the gas phase reveals that the isolated dianion [B12X11(NHC(O)H)]2- in the gas phase preferentially loses water, while the protonated form, which was generated from decomposition of the tetraalkylammonium counterion [B12X11(NHC(O)H)H]-, tends to lose carbon monoxide. Possible reaction mechanisms are discussed.

Metal Polycation Adduction to Lipids Enables Superior Ion Mobility Separations with Ultrafast Ozone-Induced Dissociation.

Specific lipid isomers are functionally critical, but their structural rigidity and usually minute geometry differences make separating them harder than other biomolecules. Such separations by ion mobility spectrometry (IMS) were recently enabled by new high-definition methods using dynamic electric fields, but major resolution gains are needed. Another problem of identifying many isomers with no unique fragments in ergodic collision-induced dissociation (CID) was partly addressed by the direct ozone-induced dissociation (OzID) that localizes the double bonds, but a low reaction efficiency has limited the sensitivity, dynamic range, throughput, and compatibility with other tools. Typically lipids are analyzed by MS as singly charged protonated, deprotonated, or ammoniated ions. Here, we explore the differential IMS (FAIMS) separations with OzID for exemplary lipids cationized by polyvalent metals. These multiply charged adducts have much greater FAIMS compensation voltages (UC) than the 1+ ions, with up to 10-fold resolution gain enabling baseline isomer separations even at a moderate resolving power of the SelexION stage. Concomitantly OzID speeds up by many orders of magnitude, producing a high yield of diagnostic fragments already in 1 ms. These capabilities can be ported to the superior high-definition FAIMS and high-pressure OzID systems to take lipidomic analyses to the next level.

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.

Impact of Protonation Sites on Collision-Induced Dissociation-MS/MS Using CIDMD Quantum Chemistry Modeling.

Protonation is the most frequent adduct found in positive electrospray ionization collision-induced mass spectra (CID-MS/MS). In a parallel report Lee, J. J. Chem. Inf. Model. 2024, 10.1021/acs.jcim.4c00760, we developed a quantum chemistry framework to predict mass spectra by collision-induced dissociation molecular dynamics (CIDMD). As different protonation sites affect fragmentation pathways of a given molecule, the accuracy of predicting tandem mass spectra by CIDMD ultimately depends on the choice of its protomers. To investigate the impact of molecular protonation sites on MS/MS spectra, we compared CIDMD-predicted spectra to all available experimental MS/MS spectra by similarity matching. We probed 10 molecules with a total of 43 protomers, the largest study to date, including organic acids (sorbic acid, citramalic acid, itaconic acid, mesaconic acid, citraconic acid, and taurine) as well as aromatic amines including uracil, aniline, bufotenine, and psilocin. We demonstrated how different protomers can converge different fragmentation pathways to the same fragment ions but also may explain the presence of different fragment ions in experimental MS/MS spectra. For the first time, we used in silico MS/MS predictions to test the impact of solvents on proton affinities, comparing the gas phase and a mixture of acetonitrile/water (1:1). We also extended applications of in silico MS/MS predictions to investigate the impact of protonation sites on the energy barriers of isomerization between protomers via proton transfer. Despite our initial hypothesis that the thermodynamically most stable protomer should give the best match to the experiment, we found only weak inverse relationships between the calculated proton affinities and corresponding entropy similarities of experimental and CIDMD-predicted MS/MS spectra. CIDMD-predicted mechanistic details of fragmentation reaction pathways revealed a clear preference for specific protomer forms for several molecules. Overall, however, proton affinity was not a good predictor corresponding to the predicted CIDMD spectra. For example, for uracil, only one protomer predicted all experimental MS/MS fragment ions, but this protomer had neither the highest proton affinity nor the best MS/MS match score. Instead of proton affinity, the transfer of protons during the electrospray process from the initial protonation site (i.e., mobile proton model) better explains the differences between the thermodynamic rationale and experimental data. Protomers that undergo fragmentation with lower energy barriers have greater contributions to experimental MS/MS spectra than their thermodynamic Boltzmann populations would suggest. Hence, in silico predictions still need to calculate MS/MS spectra for multiple protomers, as the extent of distributions cannot be readily predicted.

Mass spectrometry provides insights into the structures of polyoxovanadate alkoxide clusters substituted with Fe and W heterometals

Atom-by-atom substitution is a promising strategy for tailoring the electronic properties of transition metal oxide clusters. This approach typically generates a mixture of species that are difficult to separate using conventional methods. As a result, the characterization of their structures and electronic properties remains challenging. Herein, we use collision-induced dissociation (CID) to study the fragmentation of well-defined Fe- and W-doped Lindquist polyoxovanadate methoxides synthesized as a mixture of singly and doubly substituted species. Fragmentation reveals that Fe heteroatoms are efficiently retained within the metal oxide core. In contrast, one W atom is incorporated into the primary WO2(OCH3)2 neutral loss from both the singly and doubly substituted W-containing clusters. Collision energy-resolved CID provides insights into the fragmentation pathways, which are compared to those of the homometallic polyoxovanadate methoxide species. The incorporation of Fe into the cluster reduces its stability towards fragmentation, which could be attributed to the increase in the relative stability of Fe-containing fragment ions with four metal atoms in comparison with their homometallic analog. The observed fragmentation is rationalized by assuming that Fe atoms are incorporated within the low valent plane, while one W atom occupies the axial out-of-plane position in the cluster.