The dimer and trimer structures of the non-amyloidogenic rat islet amyloid polypeptide 21-37 peptide, formed in an H2O/CH3OH (1% CH3COOH) solution were investigated using electrospray ionization-tandem mass spectrometry (ESI-MS/MS). The dissociation of monomers, dimers, and trimers was investigated by MS/MS using collision-induced dissociation. The peptide bond dissociation between L7 and P8 was mainly observed in the tandem mass spectra of the monomers and oligomers, regardless of the parent ion charge state. The fragment ions were observed as a series of bu (u = 3-4, 6-7, 12) or yn (n = 10-11, 13-14) in the [Mono + 2H]2+ (=[monomer + 2H]2+) tandem mass spectrum. MS/MS analysis of the [Di + 3H]3+ (=[dimer + 3H]3+) complex indicated that [Di + 3H]3+ comprised [Mono + H]1+ and [Mono + 2H]2+ subunits. During covalent bond dissociation of the [Di + 3H]3+ complex, a fragmentation pattern was observed in the form of {mono + (fragment ion of [Mono + 2H]2+)}, resulting from the collision energy dissociation of the [Mono + 2H]2+ peptide. The [(C-terminal)-(C-terminal)] interaction geometry was proposed for the [Di + 3H]3+ complex based on the observation of [y10 + yn]2+ (n = 10-11, 13-16) fragment ions in the [Di + 3H]3+ tandem mass spectrum. MS/MS analysis of the [Tri + 4H]4+ (=[trimer + 4H]4+) complex indicated that [Tri + 4H]4+ comprised [Mono + H]1+ and [Di + 3H]3+ subunits. The (monomer-[Di + 3H]3+)4+ complex geometry was assumed to be stable based on the presence of {mono + (fragment ion of [Di + 3H]3+)} ions in the tandem mass spectrum of the [Tri + 4H]4+ complex. The two [Mono + (y10 + y10)]2+ and [Mono + (Mono + y10)]3+ fragment ions also supported the (monomer-[Di + 3H]3+)4+ complex geometries of the [Tri + 4H]4+ complex. The [(C-terminal)-(C-terminal)] interaction geometry of the [Di + 3H]3+ subunit is thought to be conserved in the [Tri + 4H]4+ complex geometries.

Cyclodepsipeptides (CDPs) represent a huge family of chemically and structurally diverse molecules with a wide ability for molecular interactions. CDPs are cyclic peptide-related natural products made up of both proteinogenic and nonproteinogenic amino acids linked by amide and ester bonds. The combined use of different analytical methods is required to accurately determine their integral structures including stereochemistry, thus allowing deeper insights into their often-intriguing bioactivities and their possible usefulness. Our goal is to present the various methods developed to accurately characterize CDPs. Presently, Marfey\'s method and NMR (nuclear magnetic resonance) are still considered the best for characterizing CDP configuration. Nevertheless, electrospray-high resolution tandem mass spectrometry (ESI-HRMS/MS) is of great value for efficiently resolving CDP\'s composition and sequences. For instance, recent data shows that the fragmentation of cationized CDPs (e.g., [M + Li]+ and [M + Na]+) leads to selective cleavage of ester bonds and specific cationized product ions (b series) useful to get unprecedented sequence information. Thus, after a brief presentation of their structure, biological functions, and biosynthesis, we also provide a historic overview of these various analytical approaches as well as their advantages and limitations with a special emphasis on the emergence of methods based on HRMS/MS through recent fundamental works and applications.

In this work, we employed a new ambient ionization mass spectrometry technique, sandpaper spray mass spectrometry (SPS-MS), as an efficient tool to analyze pills and tablets of pharmaceutical formulations. The following samples were analyzed: regulators of blood pressure, cholesterol, and diabetes, and drugs for the treatment of erectile dysfunction (ED). Additionally, a hard candy of Cannabis sativa containing Δ9-tetrahydrocannabinol (Δ9-THC) and its related isomer cannabidiol (CBD) was also evaluated. The surfaces of the samples, without any prior treatment, were sanded onto triangular-cut sandpaper, and full MS scans (and MS/MS) were acquired in both positive and negative ionization modes. SPS-MS (and MS/MS) allowed for prompt detection of the active pharmaceutical ingredients (APIs) in each formulation. Other components of the formulations, added as excipients, were also tentatively identified. The results described herein indicate that the SPS-MS technique can be applied to fast screening of pills and tablets being potentially used as an efficient tool to detect counterfeit pharmaceutical and illicit products, a current issue of increasing concern.

A recently published untargeted metabolomics approach toward marker compounds of cocoa germination revealed and identified 12-hydroxyjasmonic acid sulfate, (+)-catechin, and (-)-epicatechin as the most downregulated compounds and two hydroxymethylglutaryl glucosides (HMG gluc) A and B, among others, as the decisive upregulated compounds in the germinated material. These findings were quantitatively evaluated using ultrahigh-performance liquid chromatography-tandem mass spectrometry not only in previously examined sample material but also in a vastly expanded array of cocoa samples of different provenience and process and in cocoa products such as cocoa liquor and chocolate. Hereby, yields of newly identified HMG gluc derivatives could be determined in raw, fermented, germinated, and alternatively processed cocoa, and isomers of HMG gluc A and B could be established as key process indicators. Based on unsupervised clustering and supervised classification, models could identify germinated samples in testing sets consisting of raw, fermented, and germinated samples.

Phosphoesterification is the only naturally occurring covalent starch modification identified to date, and it has a major impact on overall starch metabolism. The incorporation of phosphate groups mediated by dikinases [α-glucan, water dikinase (GWD), EC 2.7.9.4; phosphoglucan, water dikinase (PWD), EC 2.7.9.5] massively alters the starch granule properties; however, previous studies did not determine whether the starch-related dikinases bind the phosphate to the glucosyl units within the amylopectin molecules in a specific pattern or randomly. In order to answer this challenging question, a number of approaches were initially pursued until a protocol could be established that enabled a massive step forward in the in vitro analysis of phosphorylated glucan chains obtained from starch. For this purpose, phosphorylation by GWD was investigated, including the final state of phosphorylation i.e., the state of substrate saturation when GWD lacks further free hydroxyl groups at OH-C6 for the catalysis of monophosphate esters. Since the separated phosphorylated glucan chains were required for the analysis, isoamylase digestion was performed to cleave the α-1,6-glycosidic bonds and to allow for the removal of the huge number of existing neutral chains by means of anion exchange chromatography. Via Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) MS and MALDI-MS/MS, the phosphorylated α-glucan chains were analysed, and the position of the phosphate group within the chain in relation to the reducing end was determined. Here, we demonstrate a protocol that enables the analysis of phosphorylated oligosaccharides, even in small quantities.

Chromatographic analysis of phenolic phytochemicals in foods has significantly advanced over the past decade (2014-2024), meeting increasing demands for precision and efficiency. This review covers both conventional and advanced chromatographic techniques used for detecting phenolic phytochemicals in foods. Conventional methods like High-Performance Liquid Chromatography, Ultra High-Performance Liquid Chromatography, Thin-Layer Chromatography, and Gas Chromatography are discussed, along with their benefits and limitations. Advanced techniques, including Hydrophilic Interaction Liquid Chromatography, Nano-LC, Multidimensional Liquid Chromatography, and Capillary Electrophoresis, are highlighted for their innovations and improved capabilities. The review addresses challenges in current chromatographic methods, emphasizing the need for standardized and validated procedures according to the Food and Drug Administration, European Cooperation for Accreditation of Laboratories, and The International Organization for Standardization guidelines to ensure reliable and reproducible results. It also considers novel strategies for reducing the environmental impact of chromatographic methods, advocating for sustainable practices in analytical chemistry.

Even though they share many thematical overlaps, plant metabolomics and stable isotope ecology have been rather separate fields mainly due to different mass spectrometry demands. New high-resolution bioanalytical mass spectrometers are now not only offering high-throughput metabolite identification but are also suitable for compound- and intramolecular position-specific isotope analysis in the natural isotope abundance range. In plant metabolomics, label-free metabolic pathway and metabolic flux analysis might become possible when applying this new technology. This is because changes in the commitment of substrates to particular metabolic pathways and the activation or deactivation of others alter enzyme-specific isotope effects. This leads to differences in intramolecular and compound-specific isotope compositions. In plant isotope ecology, position-specific isotope analysis in plant archives informed by metabolic pathway analysis could be used to reconstruct and separate environmental impacts on complex metabolic processes. A technology-driven linkage between the two disciplines could allow to extract information on environment-metabolism interaction from plant archives such as tree rings but also within ecosystems. This would contribute to a holistic understanding of how plants react to environmental drivers, thus also providing helpful information on the trajectories of the vegetation under the conditions to come.

BACKGROUND: Many phenolic C-glycosides possess nutritional benefits and pharmacological efficacies. However, the MS/MS fragmentation pattern of phenolic C-glycosides analysis is understudied. This paper aims to determine the MS/MS fragmentation patterns of phenolic C-glycosides.
METHODS: Ten compounds with different sugar moieties, aglycones, and substitutes were analyzed to determine the impact of these structural features on MS/MS fragmentation using UPLC-QTOF-MS analysis.
RESULTS: The results showed that water loss followed by RDA reaction and alpha cleavage in the C-C bonded sugar moieties are the major fragmentation pathways. Additionally, the sugar cleavage was not affected by the skeleton and the substitute of the aglycones. These results suggested that the fragmentation patterns of phenolic C-glycosides differ from those in the O-glycosides, where the O-C glycosidic bond is the most cleavage-liable bond in MS/MS analysis.
CONCLUSIONS: These MS/MS fragmentation patterns can be used for the identification of C-glycosides from dietary components and herbal medicine as well as developing robust methods using MRM methods to quantify C-glycosides.

Biological interpretation of untargeted LC-MS-based metabolomics data depends on accurate compound identification, but current techniques fall short of identifying most features that can be detected. The human fecal metabolome is complex, variable, incompletely annotated, and serves as an ideal matrix to evaluate novel compound identification methods. We devised an experimental strategy for compound annotation using multidimensional chromatography and semiautomated feature alignment and applied these methods to study the fecal metabolome in the context of fecal microbiota transplantation (FMT) for recurrent C. difficile infection. Pooled fecal samples were fractionated using semipreparative liquid chromatography and analyzed by an orthogonal LC-MS/MS method. The resulting spectra were searched against commercial, public, and local spectral libraries, and annotations were vetted using retention time alignment and prediction. Multidimensional chromatography yielded more than a 2-fold improvement in identified compounds compared to conventional LC-MS/MS and successfully identified several rare and previously unreported compounds, including novel fatty-acid conjugated bile acid species. Using an automated software-based feature alignment strategy, most metabolites identified by the new approach could be matched to features that were detected but not identified in single-dimensional LC-MS/MS data. Overall, our approach represents a powerful strategy to enhance compound identification and biological insight from untargeted metabolomics data.

Aldehyde and ketone oxocarboxylic acid photoproducts were semi-quantitated in the aqueous phase after subjecting Macondo (MC252) crude oil-seawater systems to simulated solar irradiation. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) was applied after derivatizing the samples with 2,4-dinitrophenylhydrazine (DNPH). Oil-seawater was irradiated at 27.0 °C using a solar simulator for 1 to 18 h. Following irradiation, the aqueous phase was treated with DNPH to generate aldehyde-DNPH and ketone-DNPH derivatives. Solid-phase extraction enriched the samples before analyzing them using (-) ESI-MS/MS. Precursor and product ion spectra were used to select carboxylic acid-containing aldehydes and ketones and provide semi-quantitation using surrogate standards and an internal standard. Loss of m/z 44 (CO2) in the product ion spectra further confirmed the carboxylic acid character. Near-linear increases in photoproduct concentration in the aqueous phase were observed over the 18 h irradiation period. Among the aldehyde and ketone oxocarboxylic acid photoproducts studied, photoproduction rates ranged from 0.6 - 69 µmol/h·m2 of oil surface. Despite some fluctuations, a general trend of lower production rate with higher molecular weight was observed. These results demonstrate the near-linear dependence of photoproduction on irradiance and provide ranges of rates that can be applied to modeling aldehyde and ketone oxocarboxylic acid photoproduction in ocean spills. STATEMENT OF ENVIRONMENTAL IMPACT: Crude oil on seawater degrades when exposed to sunlight. Oxygenated molecules are produced, including carboxylic acid-containing aldehydes and ketones. The formation of these photoproducts from oil films behaves linearly with solar exposure time. These photoproducts are more soluble than the original oil molecules, allowing them to have increased bioavailability and potentially increased toxicity. The rate of formation of these species when oil is exposed to sunlight determines their environmental impact.