Search Results (9)

The rapid and accurate annotation of the complex compounds and metabolites in natural products remains a significant challenge. In this study, we developed an integrated strategy to efficiently and accurately profile both the prototypes and metabolites of natural products in vivo. And this was achieved by establishing a gypenosides constituent database and utilizing R programming language to combine sample selection, virtual metabolite database construction, polygon mass defect filtering, and Kendrick mass defect filtering. In addition, the annotation strategy was successfully applied to identify the prototypes and metabolites of gypenosides in mice serum. As a case study, gypenoside LXXV was used to validate the feasibility of this approach. The results demonstrated 36 prototypes and 108 metabolites were annotated from the serum by the established annotation strategy. The prototype and eight metabolites of gypenoside LXXV were further confirmed, indicating that the proposed strategy is available. This study provides a novel approach for the rapid and accurate identification of prototypes and metabolites of natural products and offers new insights into the metabolic processes of gypenosides in vivo. Full article

Background: Among abiotic stresses to agricultural crops, drought stress is the most prolific and has worldwide detrimental impacts. The soybean (Glycine max) is one of the most important sources of nutrition to both livestock and humans. Different plant introductions (PI) of soybeans have been identified to have different drought tolerance levels. Objectives: Here, two soybean lines, Pana (drought sensitive) and PI 567731 (drought tolerant) were selected to identify chemical compounds and pathways which could be targets for metabolomic analysis induced by abiotic stress. Methods: Extracts from the two lines are analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The high mass resolution and accuracy of the method allows for identification of ions from hundreds of different compounds in each cultivar. The exact m/z of these species were filtered through SoyCyc and the Human Metabolome Database to identify possible molecular formulas of the ions. Next, the exact m/z values were converted into Kendrick masses and their Kendrick mass defects (KMD) computed, which were then sorted from high to low KMD. This latter process assists in identifying many additional molecular formulas, and is noted to be particularly useful in identifying formulas whose mass difference corresponds to two hydrogen atoms. Results: In this study, more than 460 ionic formulas were identified in Pana, and more than 340 ionic formulas were identified in PI 567731, with many of these formulas reported from soybean for the first time. Conclusions: Using the SoyCyc matches, the metabolic pathways from each cultivar were compared, providing lists of molecular targets available to profile effects of abiotic stress on these soybean cultivars. Key metabolites include chlorophylls, pheophytins, mono- and diacylglycerols, cycloeucalenone, squalene, and plastoquinones and involve pathways which include the anabolism and catabolism of chlorophyll, glycolipid desaturation, and biosynthesis of phytosterols, plant sterols, and carotenoids. Full article

Polyglycolic acid (PGA) is a biologically friendly material with a wide range of applications. The production of dimethyl oxalate using coal-based syngas and the hydrogenation of dimethyl oxalate can produce the polymerization raw material of PGA, glycolide, which requires a methyl glycolate polymerization and depolymerization process. The intermediate products of the production process were analyzed using gas chromatogram-mass spectrometry (GC-MS) and Orbitrap mass spectrometry (Orbitrap MS), which revealed the presence of cyclic and linear PGAs with different capped ends. The impurities present in the oligomer were mostly methyl-capped PGA and were retained in the subsequent depolymerization process to glycolide, solvent washing can be used to remove this part of the impurity and ultimately obtain a refined glycolide product. Furthermore, it is proposed that the use of the specialized Kendrick Mass Defect (KMD) to plot and analyze PGA compounds obtained using mass spectrometry can enable the direct classification of PGAs without the need for exact molecular formula assignment. Full article

Metabolomics is an interdisciplinary field that aims to study all metabolites < 1500 Da that are ubiquitously found within all organisms. Metabolomics is experiencing exponential growth and commonly relies on high-resolution mass spectrometry (HRMS). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a form of HRMS that is particularly well suited for metabolomics research due to its exceptionally high resolution (10⁵–10⁶) and sensitivity with a mass accuracy in parts per billion (ppb). In this regard, FT-ICR-MS can provide valuable insights into the metabolomics analysis of complex biological systems due to unique capabilities such as the easy separation of isobaric and isomeric species, isotopic fine structure analysis, spatial resolution of metabolites in cells and tissues, and a high confidence (<1 ppm mass error) in metabolite identification. Alternatively, the large and complex data sets, long acquisition times, high cost, and limited access mainly through national mass spectrometry facilities may impede the routine adoption of FT-ICR-MS by metabolomics researchers. This review examines recent applications of FT-ICR-MS metabolomics in the search for clinical and non-human biomarkers; for the analysis of food, beverage, and environmental samples; and for the high-resolution imaging of tissues and other biological samples. We provide recent examples of metabolomics studies that highlight the advantages of FT-ICR-MS for the detailed and reliable characterization of the metabolome. Additionally, we offer some practical considerations for implementing FT-ICR-MS into a research program by providing a list of FT-ICR-MS facilities and by identifying different high-throughput interfaces, varieties of sample types, analysis methods (e.g., van Krevelen diagrams, Kendrick mass defect plot, etc.), and sample preparation and handling protocols used in FT-ICR-MS experiments. Overall, FT-ICR-MS holds great promise as a vital research tool for advancing metabolomics investigations. Full article

Analysis of the heavy fractions in crude oil has been important in petroleum industries. It is well known that heavy fractions such as vacuum gas oils (VGOs) include heteroatoms, of which sulfur and nitrogen are often characterized in many cases. We conducted research regarding the molecular species analysis of VGOs. Further refine processes using VGOs are becoming important when considering carbon recycling. In this work, we attempted to classify compounds within VGOs provided by Kuwait Institute for Scientific Research. Two VGOs were priorly distillated from Kuwait Export crude and Lower Fars crude. Quantitative analysis was performed mainly using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOFMS). MALDI-TOF-MS has been developed for analyzing high-molecular-weight compounds such as polymer and biopolymers. As matrix selection is one of the most important aspects in MALDI-TOFMS, the careful selection of a matrix was firstly evaluated, followed by analysis using a Kendrick plot with nominal mass series (z*). The objective was to evaluate if this work could provide an effective classification of VGOs compounds. The Kendrick plot is a well-known method for processing mass data. The difference in the Kendrick mass defect (KMD) between C_nH_2n−14S and C_nH_2n−20O is only 0.0005 mass units, which makes it difficult in general to distinguish these compounds. However, since the z* value showed effective differences during the classification of these compounds, qualitative analysis could be possible. The analysis using nominal mass series showed the potential to be used as an effective method in analyzing heavy fractions. Full article

Automotive formulated lubricants are high value products composed of 80% base oil and 20% various additives. During their life service, lubricants are exposed to several factors that will cause degradation over time, such as high temperature, shear, and oxidation. Base oil is a complex combination of hydrocarbons that are relatively sensitive to oxidation. During the initiation phase of oxidation, free radicals are formed, leading to the production of hydroperoxide ROOH and an alkyl radical R^•. These compounds will react with the base oil molecules to form aldehydes, ketones, and carboxylic acids in the termination phase. Owing to the molecular complexity of these mixtures, Fourier transform mass spectrometry seems to be the most appropriate tool to cover their wide range of compounds due to its ultra-high resolving power and mass accuracy. In this study, a native formulated lubricant and its different oxidized states at 140 °C under air flow (3, 5, 7, 8, and 9 days of oxidation) were analyzed by FTICR MS. The combination of atmospheric pressure chemical ionization (APCI) was used to achieve a non-selective ionization of molecules, including base oils, while Electrospray ionization (ESI) was used to selectively ionize acidic molecules. Apparent Kendrick mass defect (aKMD) plots were used to separate homologous series of molecules on different horizontal lines on the basis of the CH₂ repetition unit. Aging of lubricants was mainly characterized by a rapid consumption of certain additive families, such as molybdenum dithiocarbamates (MoDTCs) and zinc dithiophosphate (ZnDTPs), but also by the emergence of many oxidation products. Thus, the presence of aldehydes, ketones, and acids was characterized in the early stage of aging while larger products from polymerization were observed in a more advanced stage of aging. Interaction products between peroxy radicals and hindered phenols/alkyl diphenylamines (ADPAs) antioxidations were elucidated toward the high m/z. The formation of such products can be explained by trapping mechanisms of these additives at high temperature (>120 °C). Other types of interaction products were observed with the formation of antioxidant complexes. Additive degradation products were also characterized. For instance, polyisobutenyl succinimide dispersant oxidation products were clearly evidenced on the aKMD plots due to the gaps of 56 Da between each point. Overall, this study demonstrated the efficiency of the aKMD approach, and the use of ESI/APCI to characterize base oil and additive oxidation products. Full article

Nearly 5% of the Shenqi Fuzheng Injection’s dry weight comes from the secondary metabolites of Radix codonopsis and Radix astragali. However, the chemical composition of these metabolites is still vague, which hinders the authentication of Shenqi Fuzheng Injection (SFI). Ultra-high performance liquid chromatography with a charged aerosol detector was used to achieve the profiling of these secondary metabolites in SFI in a single chromatogram. The chemical information in the chromatographic profile was characterized by ion mobility and high-resolution mass spectrometry. Polygonal mass defect filtering (PMDF) combined with Kendrick mass defect filtering (KMDF) was performed to screen potential secondary metabolites. A total of 223 secondary metabolites were characterized from the SFI fingerprints, including 58 flavonoids, 71 saponins, 50 alkaloids, 30 polyene and polycynes, and 14 other compounds. Among them, 106 components, mainly flavonoids and saponins, are contributed by Radix astragali, while 54 components, mainly alkaloids and polyene and polycynes, are contributed by Radix codonopsis, with 33 components coming from both herbs. There were 64 components characterized using the KMDF method, which increased the number of characterized components in SFI by 28.70%. This study provides a solid foundation for the authentification of SFIs and the analysis of its chemical composition. Full article

Base-catalyzed depolymerization of black liquor retentate (BLR) from the kraft pulping process, followed by ultrafiltration, has been suggested as a means of obtaining low-molecular-weight (LMW) compounds. The chemical complexity of BLR, which consists of a mixture of softwood and hardwood lignin that has undergone several kinds of treatment, leads to a complex mixture of LMW compounds, making the separation of components for the formation of value-added chemicals more difficult. Identifying the phenolic compounds in the LMW fractions obtained under different depolymerization conditions is essential for the upgrading process. In this study, a state-of-the-art nontargeted analysis method using ultra-high-performance supercritical fluid chromatography coupled to high-resolution multiple-stage tandem mass spectrometry (UHPSFC/HRMSⁿ) combined with a Kendrick mass defect-based classification model was applied to analyze the monomers and oligomers in the LMW fractions separated from BLR samples depolymerized at 170–210 °C. The most common phenolic compound types were dimers, followed by monomers. A second round of depolymerization yielded low amounts of monomers and dimers, while a high number of trimers were formed, thought to be the result of repolymerization. Full article

Pseudomonas species are metabolically robust, with capacity to produce secondary metabolites including cyclic lipopeptides (CLPs). Herein we conducted a chemical analysis of a crude CLP extract from the cocoyam rhizosphere-derived biocontrol strain Pseudomonas sp. COW3. We performed in silico analyses on its whole genome, and conducted in vitro antagonistic assay using the strain and purified CLPs. Via LC-MS and NMR, we elucidated the structures of four novel members of the bananamide group, named bananamides D-G. Besides variability in fatty acid length, bananamides D-G differ from previously described bananamides A-C and MD-0066 by the presence of a serine and aspartic acid at position 6 and 2, respectively. In addition, bananamide G has valine instead of isoleucine at position 8. Kendrick mass defect (KMD) allowed the assignment of molecular formulae to bananamides D and E. We unraveled a non-ribosomal peptide synthetase cluster banA, banB and banC which encodes the novel bananamide derivatives. Furthermore, COW3 displayed antagonistic activity and mycophagy against Pythium myriotylum, while it mainly showed mycophagy on Pyricularia oryzae. Purified bananamides D-G inhibited the growth of P. myriotylum and P. oryzae and caused hyphal distortion. Our study shows the complementarity of chemical analyses and genome mining in the discovery and elucidation of novel CLPs. In addition, structurally diverse bananamides differ in their antimicrobial activity. Full article