Collision-Induced Dissociation Mass Spectrometry: A Powerful Tool for Natural Product Structure Elucidation

Metabolism mechanism of glycosaminoglycans by the gut microbiota: Bacteroides and lactic acid bacteria: A review

Glycosaminoglycans (GAGs), as a class of biopolymers, play pivotal roles in various biological metabolisms such as cell signaling, tissue development, cell apoptosis, immune modulation, and growth factor activity. They are mainly present in the colon in free forms, which are essential for maintaining the host's health by regulating the colonization and proliferation of gut microbiota. Therefore, it is important to explain the specific members of the gut microbiota for GAGs' degradation and their enzymatic machinery in vivo. This review provides an outline of GAGs-utilizing entities in the Bacteroides, highlighting their polysaccharide utilization loci (PULs) and the enzymatic machinery involved in chondroitin sulfate (CS) and heparin (Hep)/heparan sulfate (HS). While there are some variations in GAGs' degradation among different genera, we analyze the reputed GAGs' utilization clusters in lactic acid bacteria (LAB), based on recent studies on GAGs' degradation. The enzymatic machinery involved in Hep/HS and CS metabolism within LAB is also discussed. Thus, to elucidate the precise mechanisms utilizing GAGs by diverse gut microbiota will augment our understanding of their effects on human health and contribute to potential therapeutic strategies for diseases.

Innovative direct introduction-ion mobility-mass spectrometry (DI-IM-MS) approach for fast and robust isomer-specific quantification in a complex matrix: Application to 2'-fucosyllactose (2'-FL) in breast milk

Identification and specific quantification of isomers in a complex biological matrix by mass spectrometry alone is not an easy task due to their identical chemical formula and therefore their same mass-to-charge ratio (m/z). Here, the potential of direct introduction combined with ion mobility-mass spectrometry (DI-IM-MS) for rapid quantification of isomers as human milk oligosaccharides (HMOs) was investigated. Differences in HMO profiles between various analyzed breast milk samples were highlighted using the single ion mobility monitoring (SIM2) acquisition for high ion mobility resolution detection. Furthermore, the Se+ (secretor) or Se- (non-secretor) phenotype could be assigned to breast milk samples studied based on their HMO contents, especially on the response of 2'-fucosyllactose (2'-FL) and lacto-N-fucopentaose I (LNFP I). The possibility of quantifying a specific isomer in breast milk by DI-IM-MS was also investigated. The standard addition method allowed the determination of the 2'-FL despite the presence of other oligosaccharides, including 3-fucosyllactose (3-FL) isomer in breast milk. This proof-of-concept study demonstrated the high potential of such an approach for the rapid and convenient quantification of isomers in complex mixtures.

Integrating the analysis of human biopsies using post-translational modifications proteomics

Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that make it difficult to characterize and treat disease. The search for clinical biomarkers to characterize disease mechanisms and complexity related to patient diagnoses and treatment has proven challenging. Knowledge of PTMs is fundamentally lacking. Characterization of complex human samples that clarify the role of PTMs and the microbiome in human diseases will result in new discoveries. This review highlights the key role of proteomic techniques used to characterize unknown biological functions of PTMs derived from complex human biopsies. Through the integration of diverse methods used to profile PTMs, this review explores the genetic regulation of proteoforms, cells of origin expressing specific proteins, and several bioactive PTMs and their subsequent analyses by liquid chromatography and tandem mass spectrometry.

Synthetic dyes: A mass spectrometry approach and applications

Synthetic dyes are found in a wide variety of applications today, including but not limited to textiles, foods, and medicine. The analysis of these molecules is pertinent to several fields such as forensics, environmental monitoring, and quality control, all of which require the sensitivity and selectivity of analysis provided by mass spectrometry (MS). Recently, there has been an increase in the implementation of MS evaluation of synthetic dyes by various methods, with the majority of research thus far falling under electrospray ionization and moving toward direct ionization methods. This review covers an overview of the chemistry of synthetic dyes needed for the understanding of MS sample preparation and spectral results, current fields of application, ionization methods, and fragmentation trends and works that have been reported in recent years.

Advancing PROTAC Characterization: Structural Insights through Adducts and Multimodal Tandem-MS Strategies

Proteolysis targeting chimeras (PROTACs) are specialized molecules that bind to a target protein and a ubiquitin ligase to facilitate protein degradation. Despite their significance, native PROTACs have not undergone tandem mass spectrometry (MS) analysis. To address this gap, we conducted a pioneering investigation on the fragmentation patterns of two PROTACs in development, dBET1 and VZ185. Employing diverse cations (sodium, lithium, and silver) and multiple tandem-MS techniques, we enhanced their structural characterization. Notably, lithium cations facilitated comprehensive positive-mode coverage for dBET1, while negative polarity mode offered richer insights. Employing de novo structure determination on 2DMS data from degradation studies yielded crucial insights. In the case of VZ185, various charge states were observed, with [M + 2H]2+ revealing fewer moieties than [M + H]+ due to charge-related factors. Augmenting structural details through silver adducts suggested both charge-directed and charge-remote fragmentation. This comprehensive investigation identifies frequently dissociated bonds across multiple fragmentation techniques, pinpointing optimal approaches for elucidating PROTAC structures. The findings contribute to advancing our understanding of PROTACs, pivotal for their continued development as promising therapeutic agents.

Metabolite Annotation Confidence Score (MACS): A Novel MSI Identification Scoring Tool

Mass spectrometry imaging (MSI) is an analytical technique capable of measuring and visualizing the spatial distribution of thousands of ions across a sample. Measured ions can be putatively identified and annotated by comparing their mass-to-charge ratio (m/z) to a database of known compounds. For high-resolution, accurate mass (HRAM) imaging data sets, this is commonly performed by the annotation platform METASPACE. Annotations are reported with a metabolite-signal-match (MSM) score as a measure of the annotation's confidence level. However, the MSM scores reported by METASPACE often do not reflect a reasonable confidence level of an annotation and are not assigned consistently. The metabolite annotation confidence score (MACS) is an alternative scoring system based on fundamental mass spectrometry imaging metrics (mass measurement accuracy, spectral accuracy, and spatial distribution) to generate values that reflect the confidence of a specific annotation in HRAM-MSI data sets. Herein, the MACS system is characterized and compared to MSM scores from ions annotated by METASPACE.

What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry

Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.

Structural Diversity and Biological Activity of Cyanopeptolins Produced by Nostoc edaphicum CCNP1411

Cyanopeptolins (CPs) are one of the most commonly occurring class of cyanobacterial nonribosomal peptides. For the majority of these compounds, protease inhibition has been reported. In the current work, the structural diversity of cyanopeptolins produced by Nostoc edaphicum CCNP1411 was explored. As a result, 93 CPs, including 79 new variants, were detected and structurally characterized based on their mass fragmentation spectra. CPs isolated in higher amounts were additionally characterized by NMR. To the best of our knowledge, this is the highest number of cyanopeptides found in one strain. The biological assays performed with the 34 isolated CPs confirmed the significance of the amino acid located between Thr and the unique 3-amino-6-hydroxy-2-piperidone (Ahp) on the activity of the compounds against serine protease and HeLa cancer cells.

Multistage Detection of Tetrodotoxin Traces in Diodon hystrix Collected in El Salvador

This study describes a multistage methodology to detect minute amounts of tetrodotoxin in fishes, a plan that may be broadened to include other marine organisms. This methodology was applied to porcupinefish (Diodon hystrix) collected in Punta Chiquirín, El Salvador. A three-stage approach along with post-acquisition processing was employed, to wit: (a) Sample screening by selected reaction monitoring (HPLC-MS/MS-SRM) analyses to quickly identify possible toxin presence via a LC/MS/MS API 3200 system with a triple quadrupole; (b) HPLC-HRFTMS-full scan analyses using an ion trap-Orbitrap spectrometer combined with an MZmine 2-enhanced dereplication-like workflow to collect high-resolution mass spectra; and (c) HPLC-HRMS2 analyses. This is the first time tetrodotoxin has been reported in D. hystrix specimens collected in El Salvador.

Electrochemical degradation of 17α-ethinylestradiol: Transformation products, degradation pathways and in vivo assessment of estrogenic activity

Conventional water treatment methods are not efficient in eliminating endocrine disrupting compounds (EDCs) in wastewater. Electrochemical Advanced Oxidation Processes (eAOPs) offer a promising alternative, as they electro-generate highly reactive species that oxidize EDCs. However, these processes produce a wide spectrum of transformation products (TPs) with unknown chemical and biological properties. Therefore, a comprehensive chemical and biological evaluation of these remediation technologies is necessary before they can be safely applied in real-life situations. In this study, 17α-ethinylestradiol (EE2), a persistent estrogen, was electrochemically degraded using a boron doped diamond anode with sodium sulfate (Na₂SO₄) and sodium chloride (NaCl) as supporting electrolytes. Ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry was used for the quantification of EE2 and the identification of TPs. Estrogenic activity was assessed using a transgenic medaka fish line. At optimal operating conditions, EE2 removal reached over 99.9% after 120 min and 2 min, using Na₂SO₄ and NaCl, respectively. The combined EE2 quantification and in vivo estrogenic assessment demonstrated the overall estrogenic activity was consistently reduced with the degradation of EE2, but not completely eradicated. The identification and time monitoring of TPs showed that the radical agents readily oxidized the phenolic A-ring of EE2, leading to the generation of hydroxylated and/or halogenated TPs and ring-opening products. eAOP revealed to be a promising technique for the removal of EE2 from water. However, caution should be exercised with respect to the generation of potentially toxic TPs.

Collision Induced Dissociation of Deprotonated Isoxazole and 3-Methyl Isoxazole via Direct Chemical Dynamics Simulations

Isoxazoles are an important class of organic compounds widely employed in synthesis and drug design. Fragmentation chemistry of the parent isoxazole molecule and its substituents has been the subject of several experimental and theoretical investigations. Collision induced dissociation (CID) of isoxazole and its substituents has been studied experimentally under negative ion conditions. Based on the observed reaction products, dissociation patterns were proposed. In the present work, we studied the dissociation chemistry of deprotonated isoxazole and 3-methyl isoxazole using electronic structure theory calculations and direct chemical dynamics simulations. Various deprotonated isomers of these molecules were activated by collision with an Ar atom, and the ensuing fractionation patterns were studied using on-the-fly classical trajectory simulations at the density functional B3LYP/6-31+G* level of electronic structure theory. A variety of reaction products and pathways were observed, and it was found that a nonstatistical shattering mechanism dominates the CID dynamics of these molecules. Simulation results are compared with experiments, and detailed atomic level dissociation mechanisms are presented.

Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section

The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.

Non-ergodic fragmentation upon collision-induced activation of cysteine-water cluster cations

Cysteine-water cluster cations Cys(H₂O)_3,6⁺ and Cys(H₂O)_3,6H⁺ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collision-induced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies from DFT calculations showing that clusters do not only fragment exclusively by sequential emission of single water molecules but also by the release of small water clusters. Release of clustered water is observed also in the ADMP (atom centered density matrix propagation) molecular dynamics model of small Cys(H₂O)₃⁺ and Cys(H₂O)₃H⁺ clusters. For large clusters Cys(H₂O)₆⁺ and Cys(H₂O)₆H⁺ the less computationally demanding statistical Microcanonical Metropolis Monte-Carlo method (M₃C) is used to model the experimental fragmentation patterns. We are able to detail the energy redistribution in clusters upon collision activation. In the present case, about two thirds of the collision energy redistribute via an ergodic process, while the remaining one third is transferred into a non-ergodic channel leading to ejection of a single water molecule from the cluster. In contrast to molecular fragmentation, which can be well described by statistical models, modelling of collision-induced activation of weakly bound clusters requires inclusion of non-ergodic processes.

Genetic mapping of maize metabolites using high-throughput mass profiling

Plant metabolites are the basis of human nutrition and have biological relevance in ecology. Farmers selected plants with favorable characteristics since prehistoric times and improved the cultivars, but without knowledge of underlying mechanisms. Understanding the genetic basis of metabolite production can facilitate the successful breeding of plants with augmented nutritional value. To identify genetic factors related to the metabolic composition in maize, we generated mass profiles of 198 recombinant inbred lines (RILs) and their parents (B73 and Mo17) using direct-injection electrospray ionization mass spectrometry (DLI-ESI MS). Mass profiling allowed the correct clustering of samples according to genotype. We quantified 71 mass features from grains and 236 mass features from leaf extracts. For the corresponding ions, we identified tissue-specific metabolic 'Quantitative Trait Loci' (mQTLs) distributed across the maize genome. These genetic regions could regulate multiple metabolite biosynthesis pathways. Our findings demonstrate that DLI-ESI MS has sufficient analytical resolution to map mQTLs. These identified genetic loci will be helpful in metabolite-focused maize breeding. Mass profiling is a powerful tool for detecting mQTLs in maize and enables the high-throughput screening of loci responsible for metabolite biosynthesis.

State-of-the-art glycosaminoglycan characterization

Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.

Gas-phase fragmentation of single heteroatom-incorporated Co5MS8(PEt3)6+ (M = Mn, Fe, Co, Ni) nanoclusters

Functionalization of metal-chalcogenide clusters by either replacing core atoms or by tuning the ligand is a powerful technique to tailor their properties. Central to this approach is understanding the competition between the strength of the metal-ligand and metal-metal interactions. Here, using collision-induced dissociation of atomically precise metal sulfide nanoclusters, Co₅MS₈L₆⁺ (L = PEt₃, M = Mn, Fe, Co, Ni) and Co_5-xFe_xS₈L₆⁺ (x = 1-3), we study the effect of a heteroatom incorporation on the core-ligand interactions and relative stability towards fragmentation. Sequential ligand loss is the dominant dissociation pathway that competes with ligand sulfide (LS) loss. Because the ligands are attached to metal atoms, LS loss is an unusual dissociation pathway, indicating significant rearrangement of the core prior to fragmentation. Both experiments and theoretical calculations indicate the reduced stability of Co₅MnS₈L₆⁺ and Co₅FeS₈L₆⁺ towards the first ligand loss in comparison with their Co₆S₈L₆⁺ and Co₅NiS₈L₆⁺ counterparts and provide insights into the core-ligand interaction.

Rapid quantitative analysis and suspect screening of per-and polyfluorinated alkyl substances (PFASs) in aqueous film-forming foams (AFFFs) and municipal wastewater samples by Nano-ESI-HRMS

A rapid analytical method for per- and polyfluoroalkyl substances (PFASs) combining nano-electrospray ionization and high-resolution mass spectrometry (Nano-ESI-HRMS) was developed and applied to aqueous film-forming foams (AFFFs) and wastewater samples collected from three local wastewater treatment plants (WWTPs). This method exhibited high sensitivity with lower limits of detection (LODs) of 3.2∼36.2 ng/L for 22 target PFAS analytes. In AFFF formulations, Nano-ESI-HRMS enabled the first-time detection of trifluoromethanesulfonic acid (TFMS), perfluoroethyl cyclohexanesulfonate (PFECHS), 6:2 fluorotelomer sulfonyl amido sulfonic acid (6:2 FTSAS-SO2), N-ammoniopropyl perfluoroalkanesulfonamidopropylsulfonate (N-AmP-FASAPS, n = 3-6), ketone-perfluorooctanesulfonic acid (Keto-PFOS), fluorotelomer unsaturated amide sulfonic acid (FTUAmS, n = 7), and 6:2 fluorotelomer amide (6:2 FTAm). Their structures were verified by the tandem MS analysis using collision-induced dissociation. Further, the combination of absolute and semi-quantification results revealed 16 PFASs from 9 PFAS classes as dominant AFFF constituents, accounting for 88.2∼96.5% of the total detected anionic and zwitterionic PFASs, including perfluorinated sulfonic acids (PFSAs, n = 1,4∼8), 6:2 fluorotelomer sulfonates (6:2 FTS), fluorotelomer thioether amido sulfonic acid (FTSAS, n = 6,8), fluorotelomer sulfinyl amido sulfonic acid (FTSAS-SO, n = 6,8), N-AmP-FASAPS (n = 6), 6:2 fluorotelomer sulfonamide alkylbetaine (6:2 FTAB), perfluoroalkylsulfonamido amino carboxylate (PFASAC, n = 6), 2-((perfluorooctyl)thio)acetatic acid (Thio-8:2 FTCA), and 6:2 FTAm. At WWTPs, aerobic and anaerobic biotransformation of PFAS precursors at the aeration tanks and secondary clarifiers were evident by the generation of mid/short-chain perfluoroalkyl acids, such as perfluoroheptanoic acid (PFHpA), perfluorohexanoic acid (PFHxA), perfluoropentanoic acid (PFPeA), as well as the emergence of ultrashort trifluoroacetic acid (TFA) and TFMS and several novel fluorotelomer carboxylic acids (FTCAs). Overall, Nano-ESI-HRMS enabled comprehensive PFAS quantitative analysis and suspect screening, applicable for rapid investigation and assessment of PFAS-related exposure and treatment in environmental matrixes. Our results also revealed that AFFFs and municipal wastewaters are two key sources contributing to the prevalent detection of ultrashort-chain PFASs (e.g., TFMS and TFA) in water.

Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research

Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and produce new metabolites. Microbes alter chemical disposition thus making the microbiome a natural subject of interest for toxicology. Sequencing and metabolomics technologies permit the study of microbiomes altered by acute or long-term exposure to xenobiotics. These investigations have already contributed to and are helping to re-interpret traditional understandings of toxicology. The purpose of this review is to provide a survey of the current methods used to characterize microbes within the context of toxicology. This will include discussion of commonly used techniques for conducting omic-based experiments, their respective strengths and deficiencies, and how forward-looking techniques may address present shortcomings. Finally, a perspective will be provided regarding common assumptions that currently impede microbiome studies from producing causal explanations of toxicologic mechanisms.

Mass spectrometry-based metabolomics in microbiome investigations

Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.

Structure-fragmentation study of pentacyclic triterpenoids using electrospray ionization quadrupole time-of-flight tandem mass spectrometry (ESI-QTOFMS/MS)

RATIONALE

Pentacyclic triterpenoids are secondary plant metabolites widespread in fruit peel, leaves, and stem bark. Due to their important biological activities, these compounds are widely screened using advance analytical techniques like electrospray ionization (ESI) mass spectrometry. Over the past few decades, the practice of ESI has been refined into a versatile ionization technique for a wide variety of analytes differing in their chemical makeup, size, complexity, and bimolecular stability.

METHODS

The structure-fragmentation relationships (SFRs) of 16 pentacyclic triterpenoids were studied using a positive ion ESI quadrupole time-of-flight mass spectrometry (ESI-QqTOFMS/MS) hybrid instrument.

RESULTS

ESI-QqTOFMS (positive ion mode) showed the presence of the protonated molecules [M + H]⁺ of most of analyzed compounds. Low-energy collision-induced dissociation MS/MS analysis of these molecules indicated multiple losses of water molecules and the loss of the formic acid moiety [M + H - HCOOH]⁺ and other substituents as the predominant pathway for further fragmentation. Key product ions were identified which resulted from the retro-Diels-Alder cleavage of the ring system. SFRs of all the compounds analyzed were also developed.

CONCLUSIONS

We developed a fragmentation pattern of pentacyclic triterpenoids using the ESI-QqTOFMS/MS technique. It was concluded that the formation of key product ions and loss of characteristic neutrals can give detailed insight into structural information about the basic structure and attached substituents.

Advanced tandem mass spectrometry in metabolomics and lipidomics-methods and applications

Metabolomics and lipidomics are new drivers of the omics era as molecular signatures and selected analytes allow phenotypic characterization and serve as biomarkers, respectively. The growing capabilities of untargeted and targeted workflows, which primarily rely on mass spectrometric platforms, enable extensive charting or identification of bioactive metabolites and lipids. Structural annotation of these compounds is key in order to link specific molecular entities to defined biochemical functions or phenotypes. Tandem mass spectrometry (MS), first and foremost collision-induced dissociation (CID), is the method of choice to unveil structural details of metabolites and lipids. But CID fragment ions are often not sufficient to fully characterize analytes. Therefore, recent years have seen a surge in alternative tandem MS methodologies that aim to offer full structural characterization of metabolites and lipids. In this article, principles, capabilities, drawbacks, and first applications of these "advanced tandem mass spectrometry" strategies will be critically reviewed. This includes tandem MS methods that are based on electrons, photons, and ion/molecule, as well as ion/ion reactions, combining tandem MS with concepts from optical spectroscopy and making use of derivatization strategies. In the final sections of this review, the first applications of these methodologies in combination with liquid chromatography or mass spectrometry imaging are highlighted and future perspectives for research in metabolomics and lipidomics are discussed.

Non-targeted analysis of vulgarisins by using collisional dissociation mass spectrometry for the discovery of analogues from Prunella vulgaris

Vulgarisins are members of diterpenoids with rare 5/6/4/5 ring skeleton from Prunella vulgaris Linn. (P. vulgaris). Their molecular scaffolds comprise different hydroxylation and degree of esterification. Vulgarisins have attracted many attentions in the fields of food and medicine for their potent bioactivities. Firstly, four reference compounds were analyzed by higher-energy collisional dissociation mass spectrometry (HCD MS/MS) and the fragmentation patterns for molecular scaffold were summarized. And then, a high-performance liquid chromatography/electrospray ionization/high-resolution mass spectrometry (HPLC-ESI-HR-MS) method was adopted to investigate the P. vulgaris extracts. Finally, the proposed analysis results were successfully applied to facilitate the discovery of the vulgarisins analogues from P. vulgaris. For the four reference compounds, the sodium adduct was the predominate ion in full scan. A specific fragmentation pathway of [M+Na]⁺ ions leads to produce diagnostic ions of vulgarisins at m/z 325 under HCD, which was formed through consecutive-side chains lost. Twenty-three diterpenoids, including 18 vulgarisins analogues, were identified or tentatively characterized in the botanical extracts of P. vulgaris based on their elemental constituents and characteristic fragment ion profiles. Two new vulgarisins analogues in the plant were isolated and their structures were illustrated based on extensive spectroscopic analysis using ¹D and ²D nuclear magnetic resonance (NMR) spectroscopy. The HCD MS/MS method, including the profiles of the diagnostic ions induced by characteristic fragmentation, is an effective technique for the discovery of vulgarisins analogues in P. vulgaris. The expected fragmentation pattern knowledge will also facilitate the analysis of other natural products.

Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research

Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.

Combination of HRLC-MS with MPP and GNPS data analysis to identify major constituents of MtSK inhibitory Alpinia galanga extract

Alpinia galanga (L.) Willd. (Zingiberaceae), or galangal, has been previously reported as active against Mycobacterium tuberculosis (TB) in vitro. The present study assessed a novel antitubercular mechanism of of galangal through M. tuberculosis shikimate kinase (MtSK) inhibitory assays. Sequential extractions of nonpolar solvents hexane and dichloromethane (DCM) were performed on galangal and screened in MtSK inhibitory assays to identify potential activity. Samples were then subjected to high resolution (HR) LC-MS chemical fingerprinting and analysis. Additionally, a novel approach was undertaken for galangal using methods such as mass professional profiler (MPP) and global natural products social (GNPS) molecular networking for structure elucidation.

Comprehensive Composition, Structure, and Size Characterization for Thiophene Compounds in Petroleum Using Ultrahigh-Resolution Mass Spectrometry and Trapped Ion Mobility Spectrometry

Thiophene compounds are the main concern of petroleum desulfurization, and their chemical composition and molecular configuration have critical impacts on thermodynamic and kinetic processes. In this work, atmospheric pressure chemical ionization (APCI) was employed for effective ionization of thiophene compounds in petroleum with complex matrix, in which carbon disulfide was used for generating predominant [M]^+• ions without the need of derivatization as for electrospray ionization. APCI coupled with ultrahigh-resolution mass spectrometry (UHRMS) was successfully applied to the composition characterization of thiophene compounds in both a low boiling petroleum fraction and a whole crude oil. APCI coupled with trapped ion mobility spectrometry (TIMS) was developed to determine the shape and size of thiophene compounds, providing configuration information that affects the steric hindrance and diffusion behavior of reactants in the desulfurization reaction, which has not been previously reported. Moreover, the comprehensive experimental structural data, expressed as the collision cross section (CCS) of the ions as surrogates of molecules, provided clues to the factors affecting the desulfurization reactivity of thiophene compounds. Further exploration showed that not only qualitative analysis of thiophene compounds can be achieved from the correlation between m/z and CCS, but also molecular size was found to be correlated with CCS that can be used as structural analysis. Overall, the molecular composition and dimension analysis together can provide substantial information for the desulfurization activity of thiophene compounds, facilitating the desulfurization process studies and catalyst design.

"Force iteration molecular designing" strategy for the systematic characterization and discovery of new protostane triterpenoids from Alisma Rhizoma by UHPLC/LTQ-Orbitrap-MS

Comprehensive analysis and identification of chemical components are of great significance for evaluating the efficacy and safety of herbal medicines, as well as for drug exploitation and development. Here we developed a "force iteration molecular designing" strategy, by combing a database-based in-house software for a precursor ion list (PIL) and PIL-triggered collision-induced dissociation-MS² and high-energy C-trap dissociation-MS² (PIL-CID/MS²-HCD/MS²) on an LTQ-Orbitrap mass spectrometer, aiming for the systematic characterization and discovery of new protostane triterpenoids (PTs) from Alisma Rhizoma (AR). AR was a well-known herbal remedy widely used for diarrhea, but its systematic characterization and comparison between two botanical origins have not been reported. Firstly, in-house software was developed based on force iteration, to generate a PIL that contains 483 accurate precursor ions. Secondly, to facilitate the acquisition of rich fragments and diagnostic ions sufficient for the structural elucidation of different types of PTs, a hybrid data acquisition method, namely PIL-CID/MS²-HCD/MS², was generated. Thirdly, a total of 473 PTs were rapidly characterized from two botanical origins of AR according to an established four-step interpretation method, and the common constituents were 277 with ratio 70% (277/395) and 78% (277/355) in the rhizome of Alisma plantago-aquatica and A. orientale, respectively. Finally, two new PTs were isolated and unambiguously identified by NMR verifying the feasibility of this combined data acquisition strategy. This integrated strategy could improve the efficiency in the detection of new compounds in a single run and is practical to comprehensively characterize the complex components in herbal medicines.

Structural Characterization of Isomeric Oligogalacturonan Mixtures Using Ultrahigh-Performance Liquid Chromatography-Charge Transfer Dissociation Mass Spectrometry

Pectins are natural polysaccharides made from galacturonic acid residues, and they are widely used as an excipient in food and pharmaceutical industries. The degree of methyl-esterification, the monomeric composition, and the linkage pattern are all important factors that influence the physical and chemical properties of pectins, such as the solubility. This work focuses on the successful online coupling of charge transfer dissociation-mass spectrometry (CTD-MS) with ultrahigh-performance liquid chromatography (UHPLC) to differentiate isomers of oligogalacturonans derived from citrus pectins. This work employed CTD fragmentation of the pectin mixtures in data-dependent acquisition mode. Compared to the UHPLC with collision-induced dissociation mass spectrometry (UHPLC-CID-MS), UHPLC-CTD-MS yielded fewer ambiguous ions and more structurally informative results. The developed UHPLC-CTD-MS method resulted in abundant cross-ring cleavages-and especially ^1,4X_n, ^1,5X_n, and ^2,4X_n ions-which helped to identify most of the isomers. The Gal A isomers differed only in the methyl group position along the galacturonic acid backbone. The combination of CTD in real time with UHPLC provides a new tool for the structural characterization of complex mixtures of oligogalacturonans and potentially other classes of oligosaccharides.

Simultaneous Analysis of Vanillin and Coumarin in Mangrove Plants and Commercial Food Products Using UPLC-ESI-MS/MS

Background:

Vanillin is a key constituent of natural vanilla. Usage of natural vanilla is affected due to its high price and limited supply, which leads to the use of artificial vanilla flavoring substances. Coumarin is a commonly encountered adulterant in beverage, food, and cosmetics as a flavoring and fragrance enhancer. However, coumarin has been banned for use as a food additive due to its toxic effects. To comply with the quality of vanillin in food and food products needs to be ensured.

Methods:

A rapid, simple and selective analytical method has been developed and validated using ultra-high performance liquid chromatography-tandem mass spectrometry for quantitative analysis of vanillin and coumarin. We also optimized fragmentation pattern of these metabolites while increasing collision energy to elucidate its structural information. The suitability and robustness of the method was checked by Zorbax Eclipse XDB C8 column (4.6 × 150 mm, 5 μm) using mobile phase comprising of methanol (A) and water with 0.1% formic acid (B) (90:10) with a flow rate 200 μL/min. The separation was achieved within 4.2 min with total run time of 5.0 min. The analysis was done by multiple reaction monitoring using 153/93 and 147/91 pair transition in positive electrospray ionization for vanillin and coumarin respectively.

Results:

The lower limit of quantification of vanillin and coumarin was 0.39 ng/mL and 3.9 ng/mL respectively. The intra and inter-day precisions for vanillin and coumarin were lower than 8.87 and 8.62 whereas, accuracy was within ± 2.13 and ± 1.53 respectively. The vanillin and coumarin was found to be stable under the examined conditions. This method was successfully applied for quantification of vanillin and coumarin in mangrove species and commercial food products.

Conclusion:

The described method and fragmentation pattern could be useful to direct confirmation and quality monitoring of a commercial food products assimilated with vanillin.

A mass spectrometry database for identification of saponins in plants

Saponins constitute an important class of secondary metabolites of the plant kingdom. Here, we present a mass spectrometry-based database for rapid and easy identification of saponins henceforth referred to as saponin mass spectrometry database (SMSD). With a total of 4196 saponins, 214 of which were obtained from commercial sources. Through liquid chromatography-tandem high-resolution/mass spectrometry (HR/MS) analysis under negative ion mode, the fragmentation behavior for all parent fragment ions almost conformed to successive losses of sugar moieties, α-dissociation and McLafferty rearrangement of aglycones in high-energy collision induced dissociation. The saccharide moieties produced sugar fragment ions from m/z (monosaccharide) to m/z (polysaccharides). The parent and sugar fragment ions of other saponins were predicted using the above mentioned fragmentation pattern. The SMSD is freely accessible at http://47.92.73.208:8082/ or http://cpu-smsd.com (preferrably using google). It provides three search modes ("CLASSIFY", "SEARCH" and "METABOLITE"). Under the "CLASSIFY" function, saponins are classified with high predictive accuracies from all metabolites by establishment of logistic regression model through their mass data from HR/MS input as a csv file, where the first column is ID and the second column is mass. For the "SEARCH" function, saponins are searched against parent ions with certain mass tolerance in "MS Ion Search". Then, daughter ions with certain mass tolerance are input into "MS/MS Ion Search". The optimal candidates were screened out according to the match count and match rate values in comparison with fragment data in database. Additionally, another logistic regression model completely differentiated between parent and sugar fragment ions. This function designed in front web is conducive to search and recheck. With the "METABOLITE" function, saponins are searched using their common names, where both full and partial name searches are supported. With these modes, saponins of diverse chemical composition can be explored, grouped and identified with a high degree of predictive accuracy. This specialized database would aid in the identification of saponins in complex matrices particular in the study of traditional Chinese medicines or plant metabolomics.

Comparison of Fragmentation Techniques for the Structural Characterization of Singly Charged Agrochemicals

Investigating the structure of active ingredients, such as agrochemicals and their associated metabolites, is a crucial requisite in the discovery and development of these molecules. In this study, structural characterization by electron-induced dissociation (EID) was compared to collisionally activated dissociation (CAD) on a series of agrochemicals. EID fragmentation produced a greater variety of fragment ions and complementary ion pairs leading to more complete functional group characterization compared to CAD. The results obtained displayed many more cross-ring fragmentation of the pyrimidine ring compared to the pyridine ring. Compounds that consisted of one aromatic heterocyclic moiety (azoxystrobin, fluazifop acid, fluazifop-p-butyl, and pirimiphos-methyl) displayed cross-ring fragmentation while compounds with only aromatic hydrocarbon rings (fenpropidin and S-metolachlor) displayed no cross-ring fragmentation. The advantages of high-resolution accurate mass spectrometry (HRAM MS) are shown with the majority of assignments at ppb range error values and the ability to differentiate ions with the same nominal mass but different elemental composition. This highlights the potential for HRAM MS and EID to be used as a tool for structural characterization of small molecules with a wide variety of functional groups and structural motifs.

Effects of chromatographic conditions and mass spectrometric parameters on the ionization and fragmentation of triterpene saponins of Ilex asprella in liquid chromatography-mass spectrometry analysis

High performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (HPLC-QTOF-MS) is widely used to qualitatively characterize the chemical profiles of herbal medicines, in which the generated adducts and fragments are crucial for confirming molecular ion (deprotonated/protonated ion) and deducing structure of detected components. However, how chromatographic and mass spectrometric (LC-MS) conditions/parameters affect the quantity and intensity of adducts and fragments of detected components is scarcely concerned. In present study, three types of triterpene saponins from the root of Ilex asprella (RIA) were selected as a case study to systematically investigate the effects of LC/MS conditions/parameters on their ionization and fragmentation, so as to obtain higher intensity (higher detection sensitivity) and quantity (rich information) of adducts and fragments for the characterization of components in RIA. It was found that for LC conditions, methanol as organic phase was more benefit for generating more adducts with higher intensity; formic acid as a modifier suppressed the formation of [M-2H]^2-, thus promoted the generation of other types of adducts at lower concentration but inhibited the generation when the concentration exceeded 0.1%. MS parameters affect scarcely the quantity but mainly intensity of adducts, cone voltage, source temperature and desolvation gas flow have relatively higher impacts when compared with other parameters. Collision energy affected both quantity and intensity of fragments. MS parameters at the medium value largely increased the quantity and intensity of adducts and fragments. Three-types of triterpene saponins presented structurally specific ionization and fragmentation due to their amounts of acidic substitutes. A total of 55 components were detected and definitely or tentatively identified in RIA under the optimized LC-MS conditions, among which 35 triterpene saponins were firstly discovered. This is the first report that proposes and validates a systematic approach for assessing the effects of LC/MS conditions/parameters on the ionization and fragmentation of analytes, which could be helpful for the optimization of LC-MS conditions for effective chemical profiling analysis of herbal medicines.

Ion Mobility Spectrometry and Tandem Mass Spectrometry Analysis of Estradiol Glucuronide Isomers

Estradiol is an estrogenic steroid that can undergo glucuronidation at two different sites, which results in two estradiol glucuronide regioisomers. These isomers can be produced by different enzymes and can have different biological activities before being eliminated from the body. Although there have been previous methods that can distinguish the two isomers, these methods often have long acquisition times or high cost per analysis. In this study, traveling wave ion mobility spectrometry (TWIMS) coupled with mass spectrometry (MS) was employed to separate estradiol glucuronides using alkali metal adduction in positive ion mode, where the sodiated dimer adduct provided adequate separation both in single-component standards and in two-component mixtures. Additionally, in negative ion mode, tandem mass spectrometry (MS/MS) was used to quantitatively determine the relative composition of the two isomers. This was possible due to differences in the energetic requirements for loss of the glucuronic acid, which was characterized by energy-resolved collision-induced dissociation (CID). This work demonstrated that the intensity of the glucuronic acid neutral loss product as compared with the intensity of the intact precursor ion can be used to determine the percentage of each isomer present in a mixture. Overall, TWIMS successfully separated estradiol glucuronide isomers in positive ion mode and MS/MS via CID enables relative quantitation of each isomer in negative ion mode.

Structure Elucidation of Macrolide Antibiotics Using MSn Analysis and Deuterium Labelling

The 14- and 16-membered macrolide antibiotics are an important structural class. Ubiquitously produced by a number of bacterial strains, namely actinomycetes, purification and structure elucidation of the wide array of analogs is challenging, both for discovery efforts and methodologies to monitor for byproducts, metabolites, and contaminants. Collision-induced dissociation mass spectrometry offers an attractive solution, enabling characterization of mixtures, and providing a wealth of structural information. However, interpretation of these spectra can be difficult. We present a study of 14- and 16-membered macrolide antibiotics, including MSⁿ analysis for unprecedented depth of coverage, and complimentary analysis with D₂O and H₂¹⁸O labeling to elucidate fragmentation mechanisms. These analyses contrast the behaviors of varying classes of macrolides and highlight how analogues can be identified in relation to similar structures, which will provide utility for future studies of novel macrolides, as well as impurities, metabolites, and degradation products of pharmaceuticals. Graphical Abstract.

Nutraceutical polyphenols: New analytical challenges and opportunities

Nowadays, the research for secondary metabolites with health promoting effects in countering or slowing-down chronic and degenerative diseases (e.g. cancer, cardiovascular, and neurodegenerative diseases) identify phenols and polyphenols, widespread and mostly copious in dietary plant sources, as beneficial for human health. These compounds, as intrinsically antioxidant, are claimed as nutraceuticals with preventive efficacy in offsetting oxidant species over-genesis in normal cells, and with the potential ability to halt or reverse oxidative stress-related diseases. In this context, pure (poly)phenols and/or their herbal/food complexes were found to exert both anti- and pro-oxidant activities, suggesting also a promising chemopreventive efficacy. In fact, different evidence further highlights their ability to induce apoptosis, growth arrest, DNA synthesis inhibition and/or modulation of signal transduction pathways. Indeed, a full understanding of the phenolic and polyphenolic composition of plant species, which still now represent their inestimable and worth exploring source, is an important challenge, which today can and must be favourably pursued in the consciousness that the bioactivity of a plant extract is always in its chemistry. To reach this purpose a number of new and advanced techniques are available for extraction, purification and structural identification purposes, but, taking into account how, when and where (poly)phenols are biosynthesized, their use must be highly rationalized. This is particularly true for mass spectrometry techniques which, although representing one of the most powerful tools and in continuous evolution in this era, often suffer from an automatism that does not give justice to the chemical goodness of a plant species and particularly those of nutraceutical interest. This review will deepen into polyphenol research, focusing on biosynthesis, analytical approaches for a conscious exploitability of nutraceutical plant extracts rich in antioxidant and anti-inflammatory polyphenols and/or pure isolated polyphenols.

Challenges in Identifying the Dark Molecules of Life

Metabolomics is the study of the metabolome, the collection of small molecules in living organisms, cells, tissues, and biofluids. Technological advances in mass spectrometry, liquid- and gas-phase separations, nuclear magnetic resonance spectroscopy, and big data analytics have now made it possible to study metabolism at an omics or systems level. The significance of this burgeoning scientific field cannot be overstated: It impacts disciplines ranging from biomedicine to plant science. Despite these advances, the central bottleneck in metabolomics remains the identification of key metabolites that play a class-discriminant role. Because metabolites do not follow a molecular alphabet as proteins and nucleic acids do, their identification is much more time consuming, with a high failure rate. In this review, we critically discuss the state-of-the-art in metabolite identification with specific applications in metabolomics and how technologies such as mass spectrometry, ion mobility, chromatography, and nuclear magnetic resonance currently contribute to this challenging task.

Identification of Polyphenols, Glycoalkaloids, and Saponins in Solanum scabrum Berries Using HPLC-UV/Vis-MS

Consumption safety of Solanum scabrum berries is controversial in different cultural practices and evaluation of the toxicity as well as micronutrition value relies on relevant phytochemical study. Thus, this study aimed to systematically profile the phytochemicals in the berries from different genetic sources and maturity. Using a combination of three different and complementary methods of HPLC-UV/Vis-MS or MS/MS with acid-assisted hydrolysis, a total of 54 phytochemicals were identified including polyphenols, saponins and toxic glycoalkaloids. Particularly, a broad range of glycoalkaloids of solasodine and its uncommon or potentially novel hydroxylated and methylated derivatives were reported, with the structure putatively identified based on the known scaffold-fragmentation pattern. Other identified phytochemicals included phenolic acids of chlorogenic acid and neochlorogenic acid, flavonol glycosides of quercetin and isorhamnetin, anthocyanins of petunidin, malvidin and delphinidin, and saponins of diosgenin and tigogenin. PRACTICAL APPLICATION: This study provides solutions for identifying the phytochemicals of S. scabrum berries, and unveiled for the first time a wide range of toxic glycoalkaloids of solasodine and analogues in the berries from different genetic sources and maturation stages. This work laid the foundation for prospective quantitative determination of berry phytochemicals and future toxicity and nutrition evaluation, and could also apply to facilitate screening or breeding for glycoalkaloid-deficient genotypes that can be used as new food supply.

Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications

The demand for understanding the roles genes play in biological systems has steered the biosciences into the direction the metabolome, as it closely reflects the metabolic activities within a cell. The importance of the metabolome is further highlighted by its ability to influence the genome, transcriptome, and proteome. Consequently, metabolomic information is being used to understand microbial metabolic networks. At the forefront of this work is mass spectrometry, the most popular metabolomics measurement technique. Mass spectrometry-based metabolomic analyses have made significant contributions to microbiological research in the environment and human disease. In this chapter, we break down the technical aspects of mass spectrometry-based metabolomics and discuss its application to microbiological research.

Electron-ion reaction-based dissociation: A powerful ion activation method for the elucidation of natural product structures

The structural elucidation of natural products (NPs) remains a challenge due to their structurally diversities and unpredictable functionalities, motifs, and scaffolds. Tandem mass spectrometry (MS/MS) is an effective method that assists the full elucidation of complicated NP structures. Ion activation methods play a key role in determining the fragmentation pathways and the structural information obtained from MS/MS. Electron-ion reaction-based dissociation (ExD) methods, including electron capture dissociation (ECD), electron transfer dissociation (ETD), electron-induced dissociation (EID), and electron detachment dissociation (EDD), can induce the breakage of specific chemical bonds and the generation of distinct fragment ions. This review article provides an overview of the mechanisms, instrumentation, and typical applications related to ExD MS/MS in the structural elucidation of NPs, primarly including lipids, oligosaccharides, glycoconjugates, metabolites, and pharmaceutical drugs. This work aims to reveal the capacity and potential of ExD mass spectrometry in analyzing NPs and consequently helping the NP communities to utilize the modern capabilities of MS/MS in the discovery and evaluation of novel NPs.

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

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

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation

The identification of unknown molecules has been one of the cornerstone applications of mass spectrometry for decades. This tutorial reviews the basics of the interpretation of electrospray ionization-based MS and MS/MS spectra in order to identify small-molecule analytes (typically below 2000 Da). Most of what is discussed in this tutorial also applies to other atmospheric pressure ionization methods like atmospheric pressure chemical/photoionization. We focus primarily on the fundamental steps of MS-based structural elucidation of individual unknown compounds, rather than describing strategies for large-scale identification in complex samples. We critically discuss topics like the detection of protonated and deprotonated ions ([M + H]+ and [M - H]- ) as well as other adduct ions, the determination of the molecular formula, and provide some basic rules on the interpretation of product ion spectra. Our tutorial focuses primarily on the fundamental steps of MS-based structural elucidation of individual unknown compounds (eg, contaminants in chemical production, pharmacological alteration of drugs), rather than describing strategies for large-scale identification in complex samples. This tutorial also discusses strategies to obtain useful orthogonal information (UV/Vis, H/D exchange, chemical derivatization, etc) and offers an overview of the different informatics tools and approaches that can be used for structural elucidation of small molecules. It is primarily intended for beginning mass spectrometrists and researchers from other mass spectrometry sub-disciplines that want to get acquainted with structural elucidation are interested in some practical tips and tricks.

Genome mining, isolation, chemical synthesis and biological evaluation of a novel lanthipeptide, tikitericin, from the extremophilic microorganism Thermogemmatispora strain T81

Tikitericin, a novel lanthipeptide was isolated and characterised together with its first total synthesis.

Genome mining of the New Zealand extremophilic microorganism Thermogemmatispora strain T81 indicated the presence of biosynthetic machinery to produce several different peptidic natural products. Solid-phase culture of T81 led to the isolation of tikitericin 1, a new lanthipeptide characterised by four (methyl)lanthionine bridges. The mass-guided isolation and structural elucidation of tikitericin 1 is described together with its total synthesis via Fmoc-solid-phase peptide synthesis (SPPS). The key non-canonical (methyl)lanthionine residues were synthesised in solution phase via an improved synthetic route and subsequently assembled to construct the peptide backbone using Fmoc-SPPS. N-Terminal truncated analogues of tikitericin (2–5) were also prepared in order to evaluate the contribution of each sequential ring of the polycyclic lanthipeptide to the antibacterial activity.