Fragment Ions Research Articles

Essential oils from fennel plants as valuable chemical products: gas chromatography–mass spectrometry, FTIR, quantum mechanical investigation, and antifungal activity

AbstractIn the present study, the biomass produced by fennel plants (Foeniculum vulgare Mill.) was converted to yield bioactive chemicals, and the hydrodistillation method was used to extract the essential oils (EOs) from both the leaves and the umbels. The antifungal activity of the EOs was tested using bioassay against the development of Fusarium oxysporum MW854649 and Alternaria solani MT279570. Molecular spectroscopic detection techniques were used to evaluate the EO products using gas chromatography–mass spectrometer (GC–MS) and Fourier transform infrared spectroscopy (FTIR). GC–MS equipped with single quadruple analyzers have been used to measure the electron ionization (EI) mass spectra of the primary constituents of fennel EOs at 70 eV. The main chemical compounds in the EO from leaves were anethole, estragole, D-limonene, trans-β-ocimene, and fenchone, with percentages of 37.94, 35.56, 17.46, 1.53, and 1.49%, respectively. The abundant compounds in the EO from umbels were estragole, anethole, D-limonene, fenchone, and γ-terpinene, with percentages of 51.18, 25.08, 12.22, 6.57, and 2.86%, respectively. EI mass spectral fragmentation of the major compounds D-limonene, estragole, anethole, and fenchone has been investigated. Umbels and leaf EOs at 5000 mg/L displayed the strongest suppression of fungal growth against A. solani, with values of 87.78% and 79.63%, respectively, compared to the positive control (94.44%). The EOs from umbels and leaves at 5000 mg/L showed the highest inhibition of fungal growth against F. oxysprium as compared to the positive control (94.44%), with values of 77.77% and 72.96%, respectively. All of the important ions—including a few distinctive fragment ions—have comprehensive fragmentation pathways defined. Based on EI, the main routes of fragmentation for the primary compounds have been identified. The existence of alkenes, aliphatic alcohols, ethers, carboxylic acids, ester compounds, alkanes, hydrogen-bonded alcohols, and phenols was demonstrated by the FTIR analysis of fennel EOs. On the other hand, the reactive behavior of the studied molecules has been investigated using two quantum mechanics method: the modified neglect of diatomic overlap (MNDO), a semi-empirical method, and the density functional theory (DFT)/B3LYP hybrid density functional method with the 6-311G (d, p) basis set in the ground state for gas phase. The optimum geometries have been obtained through the execution of computations and electrostatic potential. The obtained analytical and calculated results were then used to understand the activity of the studied EOs in further medical applications.

In-Electrospray source Hydrogen/Deuterium exchange coupled to multistage fragmentation for the investigation of the protonation and fragmentation pathways of gas phase ions.

Identification of molecules in complex natural matrices relies on matching the fragmentation spectra of ions under investigation and the spectra acquired for the corresponding analytical standards. Currently, there are many databases of experimentally measured tandem mass spectrometry spectra (such as NIST, MzCloud, and Metlin), and considerable progress has been made in the development of software for predicting tandem mass spectrometry fragments in silico using combinatorial, machine learning, and quantum chemistry approaches (such as MetFrag, CFM-ID, and QCxMS). However, the electrospray ionization molecules can be ionized at different sites (protonated or deprotonated), and the fragmentation spectra of such ions are different. Here, we are using the combination of the in-ESI source hydrogen/deuterium exchange reaction and MSn fragmentation for the investigation of the fragmentation pathways for different protomers of organic molecules. It is shown that the distribution of the deuterium in the fragment ions reflects the presence of different protomers. For several molecules, the distribution of deuterium was traced up to the MS5 level of fragmentation revealing many unusual and unexpected effects. For example, we investigated the loss of HF from the ciprofloxacin and norfloxacin ions and observed that for ions protonated at -COOH group, the eliminating hydrogen always comes from -NH group. When ions are protonated at another site, the elimination of hydrogen with a probability of 30% occurs from the -NH group, and with a probability of 70%, it originates from other sites on the molecule. Such effects were not described previously. Quantum chemical simulation was used for the verification of the protonated structures and simulation of the corresponding fragmentation spectra.

Study on phosphonylation and modification characteristics of organophosphorus nerve agents on multi-species and multi-source albumins

Protein adducts are vital targets for exploring organophosphorus nerve agents (OPNAs) exposure and identification, that can be used to characterize the chemical burden and initiate chemical safety measures. However, the use of protein adducts as biomarkers of OPNA exposure has developed slowly. To further promote the development of biomarkers in chemical forensics, it is crucial to expand the range of modified peptides and active sites, and describe the characteristics of OPNA adducts at specific reaction sites. This study utilized multi-species and multi-source albumins as the protein targets. We identified 56 peptides in albumins from various species (including human, horse, rat and pig), that were modified by at least two OPNAs. Diverse modification characteristics were observed in response to certain agents: including (1) multiple sites on the same peptide modified by one or more agents, (2) different reactivities at the same site in homologous albumins, and (3) different preferences at the same active sites associated with differences in the biological matrix during exposure. Our studies provided an empirical reference with rationalized underpinnings supported by estimated conformation energetics through molecular modeling.We employed different peptide markers for detection of protein adducts, as (one would do) in forensic screening for identification and quantification of chemical damage. Three characteristic peptides were screened and analyzed in human albumin, including Y287ICENQDSISSK, K438VPQVS443TPTLVEVSR, and Y162LY164EIAR. Stable fragment ions with neutral loss were found from their tandem MS/MS spectra, which were used as characteristic ions for identification and extraction of modified peptides in enzymatic digestion mixtures. Coupling these observations with computer simulations, we found that the structural stability of albumin and albumin-adduct complexes (as well as the effective force that promotes stability of different adducts) changes in the interval before and after adduct formation. In pig albumin, five active peptides existed stably in vivo and in vitro. Most of them can be detected within 30 min after OPNA exposure, and the detection window can persist about half a month. These early findings provided the foundation and rationale for utilizing pig albumin as a sampling target for rapid analysis in future forensic work.

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF

Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.

Photoionization and Dissociative Photoionization of Acetaldehyde in the 10.0-13.7 eV Range by Synchrotron Photoelectron Photoion Coincidence Spectroscopy.

Photoionization and dissociative photoionization of acetaldehyde (CH3CHO) in the 10.0-13.7 eV energy range are studied by using synchrotron radiation double imaging photoelectron photoion coincidence spectroscopy (i2PEPICO). The X2A' and A2A" electronic states of CH3CHO+ as well as the Franck-Condon gap region between these two states have been populated with several vibrational sequences and assigned in the high-resolution slow photoelectron spectrum (SPES). The adiabatic ionization energies (AIEs) of the X2A' and A2A" states are measured at 10.228±0.006 and 12.52±0.05 eV, respectively. The present results show that the X2A' state is a stable state while the A2A" state is fully dissociative to produce CH3CO+, CHO+ and CH4 + fragment ions. The 0 K appearance energies (AE0K) of CH3CO+ and CHO+ fragment ions are determined through the modeling of the breakdown diagram, i. e., AE0K(CH3CO+)=10.89±0.01 eV (including a reverse barrier of ~0.19 eV) and AE0K(CHO+)=11.54±0.05 eV. In addition, the dissociation mechanisms of CH3CHO+ including statistical dissociation, direct bond breaking and isomerization are discussed with the support of the calculated dissociation limits and transition state energies.

Investigation on the thermochemical characteristics, kinetics and evolved gases for typical kitchen waste pyrolysis

Kitchen waste is a complex biomass waste, whose composition and properties vary with factors such as source, season and region. It is challenging to classify and characterize it. A thermogravimetric and kinetic study was performed to estimate pyrolysis characteristics and gas emissions of starch, peel, nut shell, and vegetables. Samples underwent pyrolysis in the Simultaneous Thermal Analysis from room temperature to 1200 K at different heating rates of 10, 20, 30 and 50 K/min. The starch had the narrowest pyrolysis temperature range, while nut shell exhibited the highest residual rate. The average activation energy for pyrolysis process calculated using Coats–Redfern method was in order of starch > vegetable ≈ nut shell > peel. The gaseous products and typical functional groups of the released volatiles were identified using specific information from Fourier Transform Infrared Spectroscopy (FTIR) and Mass Spectrometry (MS). These primarily included small inorganic molecules, aldehydes, aromatics, ethers, furans, ketones, organic acids, and phenols. Aliphatic hydrocarbons significantly contributed to the total gas yield and were the most abundant for all samples. The characteristic ion fragment with m/z = 60 was only observed in peel and nut shell, while m/z = 58 ion fragments were exclusive to starch and vegetables. The practical research can provide theoretical basis for the resource utilization and environmental management of kitchen waste.

The use of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a data-independent acquisition high-resolution mass spectrometry approach, in forensic toxicological regimes: A review.

Sequential window acquisition of all theoretical fragment ion spectra (SWATH) is a type of high-resolution mass spectrometry that uses data-independent acquisition. Compared with more targeted acquisition schemes, the power behind this data-independent acquisition technique comes from its ability to mitigate interferences via the use of SWATH acquisition windows (Q1 quadrupole isolation windows) while still obtaining all accurate mass information. However, consistent with high-resolution mass spectrometry techniques, its routine and high throughput implementation in forensic toxicology is limited due to the complex processing power required to effectively manage the large amount of acquired data. It is therefore pivotal to create an efficient and validated identification criterion that confidently reports suspected positive detections as a confirmational technique for final reporting. This review examines all publications that implemented SWATH in a forensic toxicological framework with suggestive best practices and commonly used criteria. Seventeen publications were reviewed for extraction, liquid chromatography and mass spectrometry parameters, and more specifically for all SWATH applicable characteristics including spray voltages, collision energies and spreads, mass error, isotopic ratio difference, retention time error, and library score thresholds. Notwithstanding the challenges SWATH implementation faces for a laboratory, the technique demonstrates its potential to be utilized in routine forensic toxicology testing regimes and aids in the detection of both common and emerging novel drugs simultaneously.

Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of N-Linked Glycopeptides.

Glycosylation is a common modification across living organisms and plays a central role in understanding biological systems and disease. Our ability to probe the gylcome has grown exponentially in the past several decades. However, further improvements to the analytical toolbox available to researchers would allow for increased capabilities to probe structure and function of biological systems and to improve disease treatment. This article applies the developing technique of two-dimensional Fourier transform ion cyclotron resonance mass spectrometry to a glycoproteomic workflow for the standard glycoproteins coral tree lectin (CTL) and bovine ribonuclease B (BRB) to demonstrate its feasibility as a tool for glycoproteomic workflows. 2D infrared multiphoton dissociation and electron capture dissociation spectra of CTL reveal comparable structural information to their 1D counterparts, confirming the site of glycosylation and monosaccharide composition of the glycan. Spectra collected in 2D of BRB reveal correlation lines of fragment ion scans and vertical precursor ion scans for data collected using infrared multiphoton dissociation and diagonal cleavage lines for data collected by electron capture dissociation. The use of similar techniques for glycoproteomic analysis may prove valuable in instances where chromatographic separation is undesirable or quadrupole isolation is insufficient.

Structural Elucidation of Ubiquitin via Gas-Phase Ion/Ion Cross-Linking Reactions Using Sodium-Cationized Reagents Coupled with Infrared Multiphoton Dissociation.

Accurate structural determination of proteins is critical to understanding their biological functions and the impact of structural disruption on disease progression. Gas-phase cross-linking mass spectrometry (XL-MS) via ion/ion reactions between multiply charged protein cations and singly charged cross-linker anions has previously been developed to obtain low-resolution structural information on proteins. This method significantly shortens experimental time relative to conventional solution-phase XL-MS but has several technical limitations: (1) the singly deprotonated N-hydroxysulfosuccinimide (sulfo-NHS)-based cross-linker anions are restricted to attachment at neutral amine groups of basic amino acid residues and (2) analyzing terminal cross-linked fragment ions is insufficient to unambiguously localize sites of linker attachment. Herein, we demonstrate enhanced structural information for alcohol-denatured A-state ubiquitin obtained from an alternative gas-phase XL-MS approach. Briefly, singly sodiated ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS) cross-linker anions enable covalent cross-linking at both ammonium and amine groups. Additionally, covalently modified internal fragment ions, along with terminal b-/y-type counterparts, improve the determination of linker attachment sites. Molecular dynamics simulations validate experimentally obtained gas-phase conformations of denatured ubiquitin. This method has identified four cross-linking sites across 8+ ubiquitin, including two new sites in the N-terminal region of the protein that were originally inaccessible in prior gas-phase XL approaches. The two N-terminal cross-linking sites suggest that the N-terminal half of ubiquitin is more compact in gas-phase conformations. By comparison, the two C-terminal linker sites indicate the signature transformation of this region of the protein from a native to a denatured conformation. Overall, the results suggest that the solution-phase secondary structures of the A-state ubiquitin are conserved in the gas phase. This method also provides sufficient sensitivity to differentiate between two gas-phase conformers of the same charge state with subtle structural variations.

Demonstrating the Applicability of Proton Transfer Reaction Mass Spectrometry to Quantify Volatiles Emitted by the Mycoparasitic Fungus Trichoderma atroviride in Real Time: Monitoring of Trichoderma-Based Biopesticides.

The present study aims to explore the potential application of proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS) for real-time monitoring of microbial volatile organic compounds (MVOCs). This investigation can be broadly divided into two parts. First, a selection of 14 MVOCs was made based on previous research that characterized the MVOC emissions of Trichoderma atroviride, which is a filamentous fungus widely used as a biocontrol agent. The analysis of gas-phase standards using PTR-ToF-MS allowed for the categorization of these 14 MVOCs into two groups: the first group primarily undergoes nondissociative proton transfer, resulting in the formation of protonated parent ions, while the second group mainly undergoes dissociative proton transfer, leading to the formation of fragment ions. In the second part of this investigation, the emission of MVOCs from samples of T. atroviride was continuously monitored over a period of five days using PTR-ToF-MS. This also included the first quantitative online analysis of 6-amyl-α-pyrone (6-PP), a key MVOC emitted by T. atroviride. The 6-PP emissions of T. atroviride cultures were characterized by a gradual increase over the first two days of cultivation, reaching a plateau-like maximum with volume mixing ratios exceeding 600 ppbv on days three and four. This was followed by a marked decrease, where the 6-PP volume mixing ratios plummeted to below 50 ppbv on day five. This observed sudden decrease in 6-PP emissions coincided with the start of sporulation of the T. atroviride cultures as well as increasing intensities of product ions associated with 1-octen-3-ol and 3-octanone, whereas both these MVOCs were previously associated with sporulation in T. atroviride. The study also presents the observations and discussion of further MVOC emissions from the T. atroviride samples and concludes with a critical assessment of the possible applications and limitations of PTR-ToF-MS for the online monitoring of MVOCs from biological samples in real time.

Analyzing DNA barcoding and identifying toxins caused by neurotoxic mushroom poisoning using liquid chromatography tandem mass spectrometry

Background: Neurotoxic mushroom poisoning often exhibits rapid symptom onset, typically attributed to compounds such as Ibotenic acid, which affect the central nervous system. This study addresses a new case of mushroom-related food poisoning in southern Thailand. Objective: The objectives are to determine the presence of ibotenic acid in cases of mushroom-related food poisoning utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS) and to identify toxic Amanita species implicated in these cases. Materials and methods: Remnant mushroom samples obtained from three clinically reported cases were used. Nucleotide similarity was compared against the rRNA/ ITS databases using NCBI BLAST search. Phylogenetic analyses were conducted using maximum likelihood (ML) and FastTree approaches. LC-MS/MS was employed to separate of Ibotenic acid, determine its molecular weight and perform precursor ion fragmentation. Results: Analysis of the rRNA/ITS databases revealed a high nucleotide similarity between suspected mushroom samples and Amanita digitosa. Detailed phylogenetic analysis confirmed that mushroom samples from the three poisoning cases clustered with A. digitosa. LC-MS/MS analysis showed the presence of ibotenic acid, with precursor ion (m/z 159) and product ion (m/z 113.1) as the major toxic substances. Clinically, patients poisoned by ibotenic acid-containing mushrooms exhibited a short latent period with symptoms of nausea, vomiting, vertigo, delirium, confusion, and fatigue. Conclusion: The genus Amanita comprises both edible and inedible species that produce several lethal toxins. The report of ibotenic acid in A. digitosa is a novel finding, valuable for food safety monitoring and healthcare decision-maker. This is especially notable due to the accuracy and rapidity of the analytical process.

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses.

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

3D-MPEA: A Graph Attention Model-Guided Computational Approach for Annotating Unknown Metabolites in Interactomics via Mass Spectrometry-Focused Multilayer Molecular Networking.

The spectral matching strategy of MS2 fragment spectrograms serves as a ubiquitous method for compound characterization within the matrix. Nevertheless, challenges arise due to the deficiency of distinctions in spectra across instruments caused by coelution peak-derived fragments and incompleteness of the current spectral reference database, leading to dilemma of multidimensional omics annotation. The graph attention model embedded with long short-term memory was proposed as an optimized approach involving integrating similar MS2 spectra into molecular networks according to the isotopic ion peak cluster spacing features to collapse diverse ion species and expand the spectral reference library, which efficiently evaluated the substance capture capacity to 123.1% than classic substance perception tactics. The versatility and utility of the established annotation procedure were showcased in a study on the stimulation of pork mediated by 2,2-bis(4-hydroxyphenyl)propane and enabled the global metabolite annotation from knowns to unknowns at metabolite-lipid-protein level. On the spectra for which in silico extended spectral library search provided a group truth, 83.5-117.1% accuracy surpassed 1.2-14.3% precision after manual validation. β-Ala-His dipeptidase was first evidenced as the critical node related to the transformation of α-helical (36.57 to 35.74%) to random coil (41.53 to 42.36%) mediated by 2,2-bis(4-hydroxyphenyl)propane, ultimately triggering an augment of catalytic performance, inducing a series of oxidative stress, and further intervening in the availability of animal-derived substrates. The integration of ionic fragment feature networks and long short-term memory models allows the effective annotation of recurrent unknowns in organisms and the deciphering of unacquainted matter in multiomics.

Comparative Assessment of ESI‐MS Softness for Inorganic Complexes: How Soft is Your ESI‐MS?

Electrospray ionization mass spectrometry (ESI‐MS) is a powerful tool for identifying and characterizing organometallic and coordination compounds. However, detection of fragile structures bound by weaker intermolecular forces can be significantly limited in ESI‐MS owing to the use of relatively harsh instrument conditions and configurations. In this study, a set of tests was developed to assess the softness of ESI‐MS systems. Two variants are presented: positive ion mode, utilizing a mixture of sodium ions and triphenylphosphine oxide producing [Na(OPPh3)n]+ ions (n = 1–4), and negative ion mode, utilizing Pd(PPh3)4 and sulfonated triphenylphosphine producing [Pd(L)(PPh3)n]– ions (n = 0–2), where softer instrument conditions preserve a higher proportion of the high‐coordinate ions and harsher conditions will result in increased detection of products of ion fragmentation. The results revealed notable variations in instrument softness, which were influenced by a combination of instrument design and experimental parameters. Meticulously optimizing experimental conditions and ESI‐MS parameters is essential to achieving the softest ionization possible, ensuring reliable analysis where applicable. This study offers valuable insight through straightforward tests that can be employed to assess the suitability of an instrument for specific research needs.

Evaluation of efficacy of Dihuang Baoyuan Granules for diabetes mellitus and composition and in vivo distribution analysis based on UHPLC-LTQ-Orbitrap MS

Dihuang Baoyuan Granules is a prescription endorsed by HU Tianbao, a renowned and elderly Chinese medicine practitioner from Beijing, and has demonstrated definite clinical efficacy. The composition of this prescription is intricate as it includes 7 distinct herbal medicines. This study aims to analyze the chemical composition of Dihuang Baoyuan Granules, evaluate its efficacy in the treatment of diabetes and analyze the distribution of the drug components in the plasma, liver, and kidney after administration. The findings will serve as a reference for future research on pharmacodynamic substances of this prescription. UHPLC-LTQ-Orbitrap MS was employed to analyze the main chemical components of Dihuang Baoyuan Granules. A Waters ACQUITY Premier HSS T3 column(2.1 mm×100 mm, 1.8 μm) was used for chromatographic separation with 0.1% formic acid(A)-acetonitrile(B) as the mobile phases in a gradient elution at a flow rate of 0.3 mL·min~(-1). Electrospray ionization(ESI) source was used to acquire data in positive and negative ion modes. Furthermore, a rat model of diabetes mellitus was established by feeding with a high-sugar high-fat diet, and injection with streptozocin at a dose of 35 mg·kg~(-1), and the modeled rats were then administrated with Dihuang Baoyuan Granules. The fasting blood glucose, hemoglobin A1c, and other relevant indicators were measured, and the substances present in the plasma, liver, and kidney were identified. By reference to quasi-molecular ions, MS/MS fragment ions, MS spectra of reference substances, and compound information in available reports, 191 components were identified in Dihuang Baoyuan Granules, including 29 alkaloids, 24 flavonoids, 22 organic acids, 16 amino acids, 12 terpenes, 11 steroid saponins, 9 sugars, 8 phenylethanoid glycosides, 8 nucleosides, 2 phenylpropanoids, and 49 others compounds. Eighty-three chemical components were identified in rat plasma, 109 in the liver, and 98 in the kidney. Component identification and characterization of Dihuang Baoyuan Granules in vitro and in vivo provide efficacy information and guidance for the basic research on the pharmacodynamic substances and further clinical application of this prescription.

UPLC-Q-TOF-MSE Based Profiling of the Chemical Composition of Different Parts of Tetrastigma hemsleyanum

Objectives: The differences in chemical constituents in different parts of Tetrastigma hemsleyanum were analyzed. Methods: The contents of total phenols, total flavonoids, and polysaccharides in methanol extracts from different parts of T. hemsleyanum in Zhejiang were determined, and the chemical components of different parts of T. hemsleyanum were collected by ultra-performance liquid chromatography-tandem quadrupole-time-of-flight mass spectrometry. The differential index components of different parts of T. hemsleyanum were identified and analyzed by accurate mass-to-charge ratio of primary mass spectrometry and fragment ion of secondary mass spectrometry with reference spectrum and software database search and related literature reports. Results: A total of 20 components were identified, including 13 identified in root tubers, 7 in fibrous roots and 8 in leaves, and the structural cleavage of its compounds was analyzed. Conclusion: It provides a possibility and theoretical basis for the future use of the whole plant of T. hemsleyanum as medicine.

Differentiation of regioisomeric N-substituted meta-chlorophenylpiperazine derivatives

A series ofN,N-disubstituted piperazines were synthesized containing the structural elements of meta-chlorophenylpiperazine (mCPP) in combination with methoxybenzyl-, and dimethoxybenzyl substituents to yield nineN,N-disubstituted piperazine compounds. These nine potential designer-like drug analogs were prepared based on common designer trends and regioisomeric differentiation was based on gas chromatography-mass spectrometry (GC–MS) and gas chromatography-vapor phase infrared (GC–vpIR) studies.The compounds in this study have not been reported as drugs of abuse at this time. However, commercial availability of precursor chemicals including mCPP suggests the possibility of further designer exploration. Capillary GC separation showed the regioisomers to elute according to the position of aromatic ring substitution and/or the degree of substituent crowding on the aromatic ring. Numerous electron ionization (EI) mass spectral fragment ions occur via processes initiated by one of the two nitrogen atoms of the piperazine ring. The major EI-MS fragment ions observed in all nine spectra occur at m/z 195 from the loss of the substituted benzyl radical and the cation atm/z56 (C3H6N)+from the piperazine ring. Unique radical cations at m/z 136 and m/z 152 are characteristic of the 2,3- and 3,5-dimethoxybenzyl isomers, respectively. The vapor phase infrared spectra for all nine compounds show a strong absorption band in the 1591–1593 cm−1region indicative of the chloroaniline moiety. Numerous bands in the 1600–650 cm−1region provide data for the differentiation of the methoxy and dimethoxybenzyl ring substitution patterns. Thus, a combination of EI-MS and vapor phase IR allow for the differentiation and specific identification of each regioisomer in this study.

Metabolite identification of salvianolic acid A in rat using post collision-induced dissociation energy-resolved mass spectrometry

BackgroundAs one of the most famous natural products, salvianolic acid A (SAA) is undergoing clinical trials for the treatments of angina pectoris and coronary heart disorders. However, the in vivo metabolites of SAA have only been tentatively identified, leading to a barrier for precise therapeutical drug monitoring.MethodsUltra-high performance liquid chromatography coupled with quadrupole time of flight tandem mass spectrometry (UPLC–Qtof-MS/MS) was firstly employed to acquire high-resolution MS1 and MS2 spectra for all metabolites. Through paying special attention onto the features of ester bond dissociation, metabolism sites were restricted at certain regions. To further determine the metabolism site, such as the monomethylated products (M23, M25, and M26), post collision-induced dissociation energy-resolved mass spectrometry (post-CID ER-MS) was proposed through programming progressive exciting energies to the second collision chamber of hybrid triple quadrupole-linear ion trap mass spectrometry (Qtrap-MS) device.ResultsAfter SAA oral administration, 29 metabolites (M1–M29), including five, thirteen, and sixteen ones in rat plasma, urine, and feces, respectively, were detected in rats. The metabolism route was initially determined by applying well-defined mass fragmentation pathways to those HR-m/z values of precursor and fragment ions. Metabolism site was limited to SAF- or DSS-unit based on the fragmentation patterns of ester functional group. Through matching the dissociation trajectories of concerned 1st-generation fragment ions with expected decomposition product anions using post-CID ER-MS strategy, M23 and M25 were unequivocally assigned as 3'-methyl-SAA and 3''-methyl-SAA, and M26 was identified as 2-methyl-SAA or 3-methyl-SAA. Hydrolysis, methylation, glucuronidation, sulfation, and oxidation were the primary metabolism channels being responsible for the metabolites' generation.ConclusionTogether, the metabolism regions and sites of SAA metabolites were sequentially identified based on the ester bond dissociation features and post-CID ER-MS strategy. Importantly, the present study provided a promising way to elevate the structural identification confidence of natural products and metabolites.Graphical abstract

Response of protonated, adduct, and fragmented ions in Vocus proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToF-MS)

Abstract. Volatile organic compounds (VOCs) affect secondary pollutant formation via active chemistry. Proton-transfer-reaction mass spectrometry (PTR-MS) is one of the most important techniques to study the highly variable spatial and temporal characteristics of VOCs. The response of protonated, adduct, and fragmented ions in PTR-MS in changing instrument settings and varying relative humidity (RH) requires rigorous characterization. Herein, we present dedicatedly designed laboratory experiments conducted to investigate the response of these ions for 21 VOCs, including 12 oxygenated VOCs and 2 nitriles, using the recently developed Vocus PTR-MS. Our results show that the focusing ion–molecule reactor (FIMR) axial voltage increases sensitivity by 3 to 4 orders of magnitude but does not significantly change the fractions of protonated ions. Reducing the FIMR pressure, however, substantially increases fragmentation. Applying a high radio frequency (RF) amplitude radially to the FIMR can enhance sensitivity by 1 to 2 orders of magnitude without affecting the protonated ion fractions. The change in big segmented quadrupole (BSQ) amplitude mainly affects sensitivity and protonated ion fraction by modifying ion transmission. The relationship between sensitivity and proton-transfer reaction rate constant is complicated by the influences from both ion transmission and protonated ion fraction. The protonated ions of most VOCs studied (19 out of 21) show less than 15 % variations in sensitivity as RH increases from ∼ 5% to ∼ 85 %, except for some long-chain aldehydes which show a positive RH variation of up to 30 %. Our results suggest that the Vocus PTR-MS can reliably quantify the majority of VOCs under ambient conditions with varying RH. However, caution is advised for small oxygenates such as formaldehyde and methanol due to their low sensitivity and for long-chain aldehydes due to their slight RH dependence and fragmentation.

Aza-Prilezhaev Aziridination-Enabled Multidimensional Analysis of Isomeric Lipids via High-Resolution U-Shaped Mobility Analyzer-Mass Spectrometry.

Unsaturated lipids constitute a significant portion of the lipidome, serving as players of multifaceted functions involving cellular signaling, membrane structure, and bioenergetics. While derivatization-assisted liquid chromatography tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidome, it mainly faces challenges in efficiently labeling the carbon-carbon double bond (C═C) and differentiating isomeric lipids in full dimension. This presents a need for new orthogonal methodologies. Herein, a metal- and additive-free aza-Prilezhaev aziridination (APA)-enabled ion mobility mass spectrometric method is developed for probing multiple levels of unsaturated lipid isomerization with high sensitivity. Both unsaturated polar and nonpolar lipids can be efficiently labeled in the form of N-H aziridine without significant side reactions. The signal intensity can be increased by up to 3 orders of magnitude, achieving the nM detection limit. Abundant site-specific fragmentation ions indicate C═C location and sn-position in MS/MS spectra. Better yet, a stable monoaziridination product is dominant, simplifying the spectrum for lipids with multiple double bonds. Coupled with a U-shaped mobility analyzer, identification of geometric isomers and separation of different lipid classes can be achieved. Additionally, a unique pseudo MS3 mode with UMA-QTOF MS boosts the sensitivity for generating diagnostic fragments. Overall, the current method provides a comprehensive solution for deep-profiling lipidomics, which is valuable for lipid marker discovery in disease monitoring and diagnosis.