A Universal Sequencing System for Unknown Oligomers

<p><b>No synthetic chemical system can produce complex oligomers with fidelities comparable to biological systems. To bridge this gap, chemists must be able to </b><b>characterise</b><b> synthetic oligomers. Currently there are no tools for identifying synthetic oligomers with sequence resolution. Herein, we present a system that allows us to do omics-level sequencing for synthetic oligomers and use this to explore unconstrained complex mixtures. The system, Oligomer-Soup-Sequencing (OLIGOSS), can sequence individual oligomers in heterogeneous and polydisperse mixtures from tandem mass spectrometry (MS/MS) data. Unlike existing software, OLIGOSS can sequence oligomers with different backbone chemistries. Using an input file format, OLIG, that formalizes the set of abstract properties, any MS/MS fragmentation pathway can be defined. This has been demonstrated on four model systems of linear oligomers. OLIGOSS can screen large sequence spaces, enabling reliable sequencing of synthetic oligomeric mixtures, with false discovery rates (FDRs) of 0-1.1%, providing sequence resolution comparable to bioinformatic tools.</b></p>

A Universal Sequencing System for Unknown Oligomers

<p><b>No synthetic chemical system can produce complex oligomers with fidelities comparable to biological systems. To bridge this gap, chemists must be able to </b><b>characterise</b><b> synthetic oligomers. Currently there are no tools for identifying synthetic oligomers with sequence resolution. Herein, we present a system that allows us to do omics-level sequencing for synthetic oligomers and use this to explore unconstrained complex mixtures. The system, Oligomer-Soup-Sequencing (OLIGOSS), can sequence individual oligomers in heterogeneous and polydisperse mixtures from tandem mass spectrometry (MS/MS) data. Unlike existing software, OLIGOSS can sequence oligomers with different backbone chemistries. Using an input file format, OLIG, that formalizes the set of abstract properties, any MS/MS fragmentation pathway can be defined. This has been demonstrated on four model systems of linear oligomers. OLIGOSS can screen large sequence spaces, enabling reliable sequencing of synthetic oligomeric mixtures, with false discovery rates (FDRs) of 0-1.1%, providing sequence resolution comparable to bioinformatic tools.</b></p>

Metabolic profile of dendrobine in rats determined by ultra-high performance liquid chromatography/Quadrupole time-of-flight mass spectrometry

Aims & Objective: Dendrobine is a major alkaloid present mainly in dendrobium nobile Lindl. It has been reported to have analgesic, antipyretic, lower heart rate and blood pressure and other pharmacologic activities. Despite its critical pharmacological function, its metabolite profiling is still unclear. Methods: In this study, the in vivo metabolite profiling of dendrobine in rats was investigated using ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC/Q-TOF-MS). The metabolites were predicted using MetabolitePilotTM software with mass defect filter (MDF) technique. These predicted metabolites were further analyzed by MS2 spectra, and compared with the detailed fragmentation pathway of the dendrobine standard and literature data. Results: total of 59 metabolites were identified for the first time in rat plasma and urine after oral administration of dendrobine. Demethylated, dehydrogenated, hydroxylated, ketonizated and glucuronide were the major metabolic pathways. Conclusions: This research provides scientific and reliable support for full understanding of the metabolic fate of dendrobine in vivo.

Identification of HDACs Inhibitor E14 Metabolites Appeared in Rat Plasma, Feces and Urine by UPLC-QTOF-MS/MS

Background: The activation or overexpression of histone deacetylases (HDACs) are associated with the development of numerous cancers. The importance of HDACs in new anticancer therapeutic strategies has led researchers to develop promising anticancer drugs, design and synthesis of novel HDACs inhibitors are also in progress. E14 was synthesized and acted as selective inhibitor of HDACs I. Methods: We develop a sensitive UPLC-QTOF-MS/MS method to discover the new phase Ⅰ and Ⅱ metabolites of E14 from complex biological matrices in plasma, feces and urine of rats. Then a strategy comparing samples after administration with blank samples was applied to distinguish metabolites. The accurate measurements of the product ions obtained by high-resolution mass spectrometry, the structure of the parent drug and its detected metabolites are used to verify its fragmentation pathway and to obtain the proposed structure of the metabolites. Results: Fourteen metabolites were tentatively identified, including twelve metabolites in urine, five in plasma and one metabolite in feces. Hydroxylation, oxidation, methylation, N-demethylation, dehydration, glucuronidation, dehydroxylation and hydrolysis were the main metabolic pathways of E14. Conclusion: E14 is a drug with a variety of metabolites and metabolic pathways. E14 metabolites was excreted most in urine, indicating the main metabolic organ was kidney.

Exploring Chemical Structures From Cortex Lycii, Based on Manual and Automatic Analysis of the HPLC-Q-TOF-MS Data

Cortex Lycii, the root barks of Lycium barbarum and L. chinense, known as “di gu pi” in traditional Chinese herbal drugs, is an important ingredient of formulations used for treating a variety of diseases. During the last 3 decades, more than 70 chemical entities have been separated and purified from either the aqueous or aqueous ethyl alcohol extracts of Cortex Lycii. In this study, high-performance liquid chromatography together with quadrupole-time-of-flight mass spectrometry (MS) was employed to explore new analog structures from aqueous ethyl alcohol extracts (50%, v/v), which led us to discover 4 new phenolic amides and a new cyclic peptide. The structure-based manual screening method, on the basis of the analysis of the fragmentation pathway of the previously known compounds, was used to make a preliminary analysis of the negative total ion chromatography and negative extract ion spectra. Three ions at m/ z 472.1, 314.1, and 445.2 were assigned to phenolic amides, and by further analysis of their MS/MS data, the structure of 1, corresponding to one of them ( m/ z 314.1), was illustrated as an analog of the known compound KN1. A parent ion at m/ z 856.1 was assigned to a cyclic peptide analog (2) in the manual analysis procedure. Furthermore, the MS/MS data were profiled on the Global Natural Product Social Molecular Networking (GNPS, https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp ) workflow to weave a visualization molecular network. Three more new analog ions ( m/ z 604.3 [3], 597.3 [4], and 611.3 [5]) were found in the aggregation of KN5 and KN7, and their structures were all determined by comparisons with known compounds. This manual and networking automatic screening method may provide a sensitive and efficient procedure to facilitate the mining of novel trace components.

Traceability of Geographical Origin in Gentiana straminea by UPLC-Q Exactive Mass and Multivariate Analyses

The root of Gentiana straminea Maxim. (Gentianaceae), is officially listed as “Qin-Jiao” in the Chinese Pharmacopoeia for the treatment of rheumatic arthritis, icteric hepatitis, constipation, pain, and hypertension. To establish the geographical origin traceability in G. straminea, its chemical profiles were determined by a UPLC-Q exactive mass spectrometer, from which 43 compounds were identified by comparing retention times and mass spectrometry. Meanwhile, a pair of isomers (loganin and secologanol) was identified by mass spectrometry based on their fragmentation pathway. A total of 42 samples from difference habitats were determined by an UPLC-Q exactive mass spectrometer and the data were assayed with multivariate statistical analysis. Eight characteristic compounds were identified to determine the geographical origin of the herb. To estimate the key characteristic markers associated with pharmacological function, the inhibiting activities of nitric oxide (NO) production in lipopolysaccharide (LPS)-induced macrophages were examined. This finding is crucial in realizing the determination of botanical origin and evaluating the quality of G. straminea.

Identification and Characterization of Forced Degradation Products for Dofetilide using Rapid and Sensitive UPLC-MS/MS Method and HRMS Studies

A simple, rapid and efficient method has been developed and validated using ultra UPLC combined with Q-ToF MS system for recognition and characterization of forced degradation products obtained from dofetilide degradation studies. The dofetilide drug is an antiarrhythmic and belongs to Class III and it was treated with various stress conditions like acidic, basic, oxidative, photolytic and thermal conditions as per ICH guidelines. The main drug shows extensive degradation towards oxidative degradation conditions and single degradation product was identified through chromatogram. The chromatographic separation among main and its impurities were attained through 2.1 × 150, 1.8 μm column from gradient elution using UPLC and its detection at wavelength 230 nm. The validation was performed for the developed method using various parameters like specificity, linearity and robustness studies. Waters Synapt G2 Q TOF system was used and performed MSn studies to establish mass spectral fragmentation pathway for drug and its degradation products and determined accurate masses study. The efficiency of this method was helpful to identify and characterize the drug and degradation products using LC/MSn techniques.

A Comprehensive Review of the Structure Elucidation of Tannins from Terminalia Linn.

Objectives. Tannins with complex structures are important plant resources, which are abundant in the genus Terminalia. Various Terminalia species have been playing an important role in traditional medicine system. A systematic scoping review of Terminalia Linn. research literature for tannins was conducted to summarize the structures of tannins and analysis fragmentation pathway characteristics, which could provide references for the structural analysis of tannins from Terminalia Linn. Methods. After an update of the literature search up to September 2018, the terms of Terminalia in all publications were analyzed. Electronic searches were conducted in scifinder and PubMed, and the information from 197 articles in all with regard to the tannin structure study was extracted. Results. The compounds of 82 tannins from the genus Terminalia were reviewed. According to the structural differences, they can be divided into three categories, hydrolysable tannins, condensed tannins, and complex tannins, respectively. The fragmentation pathways of 46 identified tannins were analyzed, and the fragmentation rules of tannins were speculated according to different types. Conclusion. This review has attracted attention to the active substances in this species such as the tannins summarized in further study. How to improve the extraction and purification technology of tannins from genus Terminalia is an urgent problem to be solved.

Simultaneous Analysis of Twelve Bile Acids by UPLC-MS and Exploration of the Processing Mechanism of Bile Arisaema by Fermentation

Ultrahigh-performance liquid chromatography (UPLC) coupled with quadrupole time-of-flight tandem mass spectrometry (Q/TOF-MS) in the MS/MS mode and UPLC coupled with triple quadrupole mass spectrometry (QqQ-MS) using the multiple reaction monitoring (MRM) mode were used to make a qualitative and quantitative analysis of twelve bile acids in Bile Arisaema. The fragmentation pathway of twelve bile acids was proposed. The quantification method showed a good linearity over a wide concentration range (R2 > 0.99), repeatability (RSD < 4.12%), stability (RSD < 4.25%), precision (RSD < 4.06%), and recovery (95.36–102.15%). Content of twelve compounds in Bile Arisaema varied significantly depending on region. Chemometric methods, hierarchical clustering analysis (HCA), and principal components analysis (PCA) were successfully used to optimize the fermentation time of the Bile Arisaema. The results suggested that the Bile Arisaema could complete fermentation in 15 days. The possible processing mechanism of Bile Arisaema promoted the transformation of conjugated bile acids into free bile acids in fermentation.