Search Results (27)

This work presents an extension of the Belgrade ACol collisional database within the Virtual Atomic and Molecular Data Centre (VAMDC) framework to include dissociative electron attachment (DEA) processes. DEA, a low-energy electron-driven resonant mechanism leading to molecular fragmentation, is relevant in fields such as plasma science, radiation damage, nanofabrication, and EUV lithography. The ACol data model was redesigned to improve semantic clarity and flexibility by separating physical collision data from bibliographic and serialization structures. A new DataSource entity and a redefined TabulatedData–Collision relationship enable a more normalized database while preserving compatibility with the XSAMS schema through dynamic, query-time construction of hierarchical structures. The implementation is demonstrated using DEA to isoflurane, incorporating experimental data from independent studies and cataloging resulting fragment anions and energy-dependent yields. Elastic cross sections of isoflurane are included as they are immanently connected to DEA, providing an essential tool for understanding the complex DEA process. The novelty of the present implementation lies not in the first representation of DEA within VAMDC, but in its integration into a multi-process collision database based on a compact, normalized data model that separates scientific data and bibliographic provenance from the XSAMS serialization structure. The updated architecture enhances interoperability, reduces redundancy, and improves data management while maintaining compliance with VAMDC standards. Full article

Fragmentation Resilience Energy Mass Spectrometry (FREMS) builds on the field of energy-resolved mass spectrometry and previously used methods, e.g., Survival Yield. It exploits breakdown energies at near “continuous” ramp (0.2% NCE increments) to offer higher resolution and a reliable method for compound differentiation, contaminant identification and structural elucidation. Implementation of FREMS involves acquiring ion breakdown/formation curves as collision energy is incrementally increased. These curves themselves can be analyzed by several means to give a single metric—Fragmentation Resilience (FR₅₀). This value has been shown to be experimentally interchangeable with the modified-Survival Yield (m-SY₅₀) and the Cross-Intersect (C-I). A full panel of testing on an LTQ-Orbitrap revealed that breakdown energies depend only on three controllable parameters—number of ions inside the ion trap, Maximum Inject time and Activation Time. A fairly linear relationship (R² > 0.95) with proposed FR₅₀, m-SY₅₀ and C-I metrics provides reliable adjustment mechanisms for these variables via calibrations. Consequently, this technique can be applied to ions produced by any atmospheric pressure ionization processes and treated as exclusively in vacuo experiments. Applications of FREMS to 4-chlorobenzylpyridinium ion revealed that under collisional activated dissociation (CAD) conditions, the rate of decomposition of precursor ion is equivalent to the rate of formation of its fragments, i.e., normalized breakdown and formation curves intersect at inflection points. Full article

Background: Comprehensive and accurate compound composition characterization in natural sources has high relevance in food and nutrition, health and medicine, environmental and agriculture research areas, though profiling of plant metabolites is a challenging task due to the structural complexity of natural products. This study delves into the identification and characterization of compounds within the Plantago genus, leveraging state-of-the-art analytical techniques. Methods: Utilizing an ultra-high-performance liquid chromatography (UHPLC) system in conjunction with Orbitrap™ IQ-X™ Tribrid™ mass spectrometer (MS), we employed a Phenyl-Hexyl HPLC column alongside optimized extraction protocols to analyze both husk and leaf samples. To maximize compound identification, we implemented data-dependent acquisition (DDA) methods including MS² (ddMS2), MS³ (ddMS3), AcquireX™ deep scan, and real-time library search (RTLS). Results: Our results demonstrate a significant increase in the number of putatively yet confidently assigned compounds, with 472 matches in P. lanceolata leaves and 233 in P. ovata husk identified through combined acquisition methods. The inclusion of an additional fragmentation level (MS³) noticeably enhanced the confidence in compound annotation, facilitating the differentiation of isomeric compounds. Furthermore, the application of low-energy fragmentation (10 normalized collision energy (NCE) for higher-energy collisional dissociation (HCD)) improved the detection and grouping of MS¹ fragments by 55% in positive mode and by 16% in negative mode, contributing to a more comprehensive analysis with minimal loss in compound identification. Conclusions: These advancements underscore the potential of our methodologies in expanding the chemical profile of plant materials, offering valuable insights into natural product analysis and dereplication of untargeted data. Full article

Background/Objectives: Animal and fungal sterols and stanols exhibit remarkable structural diversity, driven by variations in the number and position of C=C bonds within the steroidal tetracyclic core and side chain, along with diverse branching patterns of the latter. Similarly to phytosterols, these metabolites produce highly complex tandem mass spectra, whose interpretation has so far been limited. To address this gap, the fragmentation behavior of selected animal/fungal sterols and stanols was studied in this paper. Methods: Higher-Collisional-energy Dissociation–High-resolution tandem mass spectrometry (HCD-HRMS/MS) of protonated/dehydrated species generated via atmospheric pressure chemical ionization (APCI) was performed on structurally diverse compounds, including lathosterol, desmosterol, zymosterol, lanosterol, ergosterol, chalinasterol, and the stanols coprostanol and cholestanol. Results: Structurally diagnostic product ions originating from the side chains were unveiled, shedding light on the intramolecular migration of positive charge from the initial ionization site at C3 to alternative stable sites across the molecular structure, which is a typical mechanism also noted in cholesterol and phytosterols. In addition, characteristic fragmentation patterns related to the steroidal backbone were found and discussed for Δ⁷, Δ^5,7 and Δ⁸-sterols, and a novel elucidation of the fragmentation behavior of 4,4-dimethyl-Δ⁸-sterols, based on lanosterol as a model compound, was achieved. The relative intensities of diagnostic product ions allowed a correlation with specific structural motifs, and “cholesterol-like” and “stigmasterol-like” fragmentations pathways were recognized. These findings were integrated with prior data on cholesterol and plant sterol fragmentation acquired under identical analytical conditions. Moreover, as a proof of its relevance for novel sterol identification, MS/MS-related information was successfully applied to the identification of a positional isomer (Δ⁷) of zymosterol in baker’s yeast extract, along with typical fungal major sterols. Conclusions: The comprehensive archive of sterol/stanol fragmentations obtained by APCI-HCD-MS/MS might prove very useful for the future characterization of novel sterol/stanol species in complex matrices. Full article

Ion interactions with molecular structures give insights into physicochemical processes in the cosmos, radiation damage, plasma, combustion, and biomass conversion reactions. At the atomic scale, these interactions lead to excitation, ionization, and dissociation of the molecular components of structures found across all these environments. Furan, cyclic aromatic ether (C₄H₄O), serves as a gas-phase deoxyribose analog and is crucial for understanding key pathways in renewable biomass conversion, as its derivatives are versatile molecules from lignocellulosic biomass degradation. Therefore, collisions of H₃⁺ and C⁺ ions with gas-phase furan molecules were investigated in the 50–1000 eV energy range, exploiting collision-induced emission spectroscopy. High-resolution fragmentation spectra measured at 1000 eV for both cations reveal similar structures, with C⁺ collisions resulting in more significant furan fragmentation. Relative cross-sections for product formation were measured for H₃⁺ + C₄H₄O collisions. Possible collisional processes and fragmentation pathways in furan are discussed. These results are compared with those for tetrahydrofuran and pyridine to illustrate how the type and charge of the projectile influence neutral fragmentation in heterocyclic molecules. Full article

Cannabinoid molecules are the family of molecules that bind to the cannabinoid receptors (CB1 and CB2) of the human body and cause changes in numerous biological functions including motor coordination, emotion, and pain reception. Cannabinoids occur either naturally in the Cannabis Sativa plant or can be produced synthetically in the laboratory. The need for accurate analytical methods for analyzing cannabinoid molecules is of considerable current importance due to demands for detecting illegal cannabinoids and for monitoring the manufacture of popular, non-illegal cannabinoid products. Mass spectrometry has been shown to be an optimum technique for identifying cannabinoids. In this work, we perform Higher Collisional Dissociation (HCD) mass spectrometric measurements on an Orbitrap Fusion Tribrid Mass Spectrometer to measure the collision-energy-dependent molecular fragmentation pathways of a group of key cannabinoids and their metabolites (cannabidiol, Δ9-Tetrahydrocannabinol, 11-Hydroxy-Δ9-tetrahydrocannabinol, 11-nor-9-Carboxy-Δ9-tetrahydrocannabinol, cannabidiolic acid, tetrahydrocannabinolic acid), along with two synthetic cannabinoids (JWH-018 and MDMB-FUBINACA). This is the first time that cannabinoid molecules have been studied using energy-resolved HCD methods. We identified a number of common, primary fragmentation pathways, including loss of water, loss of other small neutral molecule units (e.g., butene), and rupture of the central C-C bond that links the aromatic and alkyl ring groups. Quantum chemical calculations are presented to provide insights into preferred protonation sites and to characterize isomerization of protonated open-ring cannabinoids (e.g., [CBDA + H]⁺) into closed-ring analogues (e.g., [THCA + H]⁺). A key result to emerge from our study is that energy-resolved HCD measurements are particularly valuable in identifying isomerization, since the isobaric pairs of molecular ions studied here (e.g., [CBDA + H]⁺ and [THCA + H]⁺) are associated with identical HCD profiles indicating that isomerization of one structure into the other has occurred during the electrospray–mass spectrometry process. This is an important result as it will have general applicability to other tautomeric ions and thus demonstrates the application of energy-resolved HCD as a tool for identifying tautomerization proclivity. Full article

As the development of new biotherapeutics advances, increasingly sophisticated tandem mass spectrometry methods are needed to characterize the most complex molecules, including antibody drug conjugates (ADCs). Lysine-linked ADCs, such as trastuzumab-emtansine (T-DM1), are among the most heterogeneous biotherapeutics. Here, we implement a workflow that combines limited proteolysis with HCD-triggered EThcD and UVPD mass spectrometry for the characterization of the resulting middle-down large-sized peptides of T-DM1. Fifty-three payload-containing peptides were identified, ranging in mass from 1.8 to 16.9 kDa, and leading to the unambiguous identification of 46 out of 92 possible conjugation sites. In addition, seven peptides were identified containing multiple payloads. The characterization of these types of heterogeneous peptides represents an important step in unraveling the combinatorial nature of lysine-conjugated ADCs. Full article

D-amino acid-containing peptides (DAACPs) occur in biological and artificial environments. Since the importance of DAACPs has been recognized, various mass spectrometry-based analytical approaches have been developed. However, the capability of higher-energy collisional dissociation (HCD) fragmentation to characterize DAACP sites has not been evaluated. In this study, we compared the normalized spectra intensity under different conditions of HCD and used liraglutide along with its DAACPs as examples. Our results indicated that the difference in the intensity of y ions between DAACPs and all-L liraglutide could not only distinguish them but also localize the sites of D-amino acids in the DAACPs. Our data demonstrate the potential of using HCD for the site characterization of DAACPs, which may have great impact in biological studies and peptide drug development. Full article

Criegee intermediates, which are the products of the ozonolysis of alkenes, play a key role in many chemical and physical processes in the atmosphere. Their reactions with other atmospheric compounds are responsible for the formation of hydroxyl, methyl, hydrogen radicals, nitric and sulfuric acids, and others. Methane is an active greenhouse gas whose concentration has increased rapidly in the last several decades. In this work, we consider the interaction between these two important atmospheric compounds. We choose the three simple Criegee intermediate (CI) molecules: formaldehyde oxide (CH₂OO), acetaldehyde oxide (CH₃CHOO), and acetone oxide ((CH₃)₂COO). Some reactions between methane and these Cis have been studied earlier as possible pathways for deactivating methane as well as a source of methanol formation due to molecular collisions in the atmosphere. In the present study, we extend the consideration to the case when an intermediate energetically stable complex is formed after collision. We found that this complex could easily decompose to form an OH radical and another unstable fragment, which can quickly dissociate into CH₃ radicals, atomic hydrogen, acetone, acetaldehyde, propaldehyde, methyl alcohol, water, and others, depending on the type of CI being reacted with. These compounds can actively interact with other atmospheric components and change their physical and chemical properties. In addition, CI with a methyl substituent is shown to have increased energy in transition states and minima, resulting in slower reaction rates. Full article

We have studied wake effects on the dissociation of heavy quarkonia states J/ψ and Y by introducing an in-medium modification to the inter-quark potential. The wakes in the quark–gluon plasma were modeled using linear response theory using a dynamic dielectric function obtained from kinetic theory (Boltzmann equation) with a Bhatnagar–Gross–Krook (BGK) collision term. The in-medium modified potential was used to investigate the dissociation character depending on various parameters such as the velocity of quarkonium moving through the medium and the collision frequency. We have also calculated critical values of the dissociation temperature. Modifications of the dissociation energy due to wake-field effects were found. Full article

Auroral events are the prominent manifestation of solar/stellar forcing on planetary atmospheres because they are closely related to the stellar energy deposition by and evolution of planetary atmospheres. A numerical kinetic Monte Carlo model was developed with the aim to calculate the steady-state energy distribution functions of suprathermal N(⁴S) atoms in the polar upper atmosphere formed due to the precipitation of high-energy auroral electrons in the N₂-O₂ atmospheres of rocky planets in solar and exosolar planetary systems. This model describes on the molecular level the collisions of suprathermal N(⁴S) atoms and atmospheric gas taking into account the stochastic nature of collisional scattering at high kinetic energies. It was found that the electron impact dissociation of N₂ is an important source of suprathermal N atoms, significantly increasing the non-thermal production of nitric oxide in the auroral regions of the N₂-O₂ atmospheres of terrestrial-type planets. Full article

Triacylglycerol estolides (TG-EST) are biologically active lipids extensively studied for their anti-inflammatory and anti-diabetic properties. In this work, eight standards of TG-EST were synthesized and systematically investigated by nanoelectrospray tandem mass spectrometry. Mass spectra of synthetic TG-EST were studied with the purpose of enabling the unambiguous identification of these lipids in biological samples. TG-EST glycerol sn-regioisomers and isomers with the fatty acid ester of hydroxy fatty acid (FAHFA) subunit branched in the ω-, α-, or 10-position were used. Ammonium, lithium, and sodium adducts of TG-EST formed by nanoelectrospray ionization were subjected to collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD). Product ion spectra allowed for identification of fatty acid (FA) and FAHFA subunits originally linked to the glycerol backbone and distinguished the α-branching site of the FAHFA from other estolide-branching isomers. The ω- and 10-branching sites were determined by combining CID with ozone-induced dissociation (OzID). Lithium adducts provided the most informative product ions, enabling characterization of FA, hydroxy fatty acid (HFA), and FAHFA subunits. Glycerol sn-regioisomers were distinguished based on the relative abundance of product ions and unambiguously identified using CID/OzID of lithium and sodium adducts. Full article

Octyl methoxycinnamate (OMC) is a common UVA and UVB filter molecule that is widely used in commercial sunscreens. Here, we used gas-phase laser photodissociation spectroscopy to characterise the intrinsic photostability and photodegradation products of OMC by studying the system in its protonated form, i.e., [OMC·H]⁺. The major photofragments observed were m/z 179, 161, and 133, corresponding to fragmentation on either side of the ether oxygen of the ester group (m/z 179 and 161) or the C–C bond adjacent to the ester carbonyl group. Additional measurements were obtained using higher-energy collisional dissociation mass spectrometry (HCD-MS) to identify fragments that resulted from the breakdown of the vibrationally hot electronic ground state. We found that the m/z 179 and 161 ions were the main fragments produced by this route. Notably, the m/z 133 ion was not observed through HCD-MS, revealing that this product ion is only produced through a photochemical route. Our results demonstrate that UV photoexcitation of OMC is able to access a dissociative excited-state surface that uniquely leads to the rupture of the C–C bond adjacent to the key ester carbonyl group. Full article

Auroral events are the prominent manifestation of solar/stellar forcing on planetary atmospheres. They are closely related to the energy deposition by and evolution of planetary atmospheres, and their observations are widely used to analyze the composition, structure, and chemistry of the atmosphere under study, as well as energy fluxes of the precipitating particles that affect the atmosphere. A numerical kinetic Monte Carlo model had been developed, allowing us to study the processes of precipitation of high-energy auroral electrons into the N₂-O₂ atmospheres of the rocky planets in the Solar and exosolar planetary systems. This model describes on a molecular level the collisions of auroral electrons and atmospheric gas, taking into account the stochastic nature of collisional scattering at high kinetic energies. The current status of the kinetic model is illustrated in the applications to the auroral events on the Earth such as the production of suprathermal nitrogen atoms due to the electron impact dissociation of N₂. It was found that electron impact dissociation of N₂ can potentially be an important source of suprathermal N atoms in the auroral regions of the N₂-O₂ atmosphere of terrestrial-type planets. Such research will allow us to study the odd nitrogen chemistry as an atmospheric marker of the N₂-O₂ atmosphere of rocky exoplanets. Full article

In this study, we developed a high-resolution tandem mass spectrometry (HR MS) approach to assess presumed changes in gangliosidome of a human hippocampus affected by temporal lobe epilepsy (TLE) in comparison with a normal hippocampus. Gangliosides, membrane glycolipids, are particularly diverse and abundant in the human brain, and participate in ion transport and modulation of neuronal excitability. Changes in structural ganglioside pattern potentially linked to TLE molecular pathogenesis have not been explored in detail. Aiming to characterize TLE-specific gangliosidome, we analyzed the native gangliosides purified from a human hippocampal tissue sample affected by TLE and a control hippocampus using HR MS. Marked differences of ganglioside expression were shown in TLE vs. control, particularly with respect to the sialylation degree of components, discovered as a characteristic feature of TLE. Another major finding is the occurrence of tetrasialofucogangliosides in TLE and species modified by either O-acetylation or CH₃COO⁻. Structural analysis by higher-energy collisional dissociation (HCD) MS/MS gave rise to fragmentation patterns implying that the GQ1b (d18:1/18:0) isomer is specifically associated with TLE. Further investigation in a larger sample is needed in order to confirm the discovery of ganglioside structures specifically expressed in human TLE and to provide information on the probable role of gangliosides in the molecular events underlying seizures. Full article