Article
Chemistry, Applied
Veronique Bonnet, Gilles Clodic, Christian Sonnendecker, Wolfgang Zimmermann, Cedric Przybylski
Summary: In this study, it was demonstrated that ion mobility mass spectrometry (IM-MS) can effectively discriminate isomers of cyclic oligosaccharides and provide models through molecular modeling. These results are significant for the identification of carbohydrate conformers that cannot be easily reached by other approaches.
CARBOHYDRATE POLYMERS
(2023)
Review
Chemistry, Analytical
Maartje Verhoeven, Jennifer Bonetti, Ruben Kranenburg, Arian van Asten
Summary: Due to the increasing number of NPSs, identifying drug isomers is becoming more challenging for forensic laboratories. Currently, GC-MS is the standard technique, but it cannot confidently differentiate positional isomers. This review provides an overview of methods for differentiating and identifying NPS positional isomers and proposes a workflow for routine analysis in forensic laboratories.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Zuzana Stiffelova, Ladislav Moravsky, Bartosz Michalczuk, Jozef Cizmarik, Stefan Matejcik, Fils Andriamainty
Summary: This study demonstrated the separation of positional isomers of alkoxyphenylcarbamic acid derivatives using Thin Layer Chromatography (TLC) and Ion Mobility Spectrometry (IMS) with diode laser desorption. Ion mobilities increased with the change in geometry from ortho to para position of the alkoxy chain, consistent with their different collision cross sections (CCS).
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Article
Chemistry, Physical
Rylee Wander, Andrea M. Kaminski, Zhangjie Wang, Eduardo Stancanelli, Yongmei Xu, Vijayakanth Pagadala, Jine Li, Juno M. Krahn, Truong Quang Pham, Jian Liu, Lars C. Pedersen
Summary: The study presents the crystal structures of 3-OST-5 with substrates and PAP, revealing its substrate specificity and anti-factor Xa activity. The enzyme prefers to sulfate a 6-O-sulfo glucosamine saccharide that is surrounded by glucuronic acid. Additionally, it was found that substrate specificity is not only determined by the side chains of amino acid residues in the active site, but also by the conformational flexibility of 2-O-sulfated iduronic acid in the saccharide substrates.
Article
Multidisciplinary Sciences
Guifang Feng, Ming Gao, Liwei Wang, Jiayi Chen, Menglu Hou, Qiongqiong Wan, Yun Lin, Guoyong Xu, Xiaotian Qi, Suming Chen
Summary: The authors developed a workflow for deep structural lipidomics to simultaneously identify the position and configuration of double bonds in unsaturated lipids, providing a powerful tool for exploring lipid structural biology.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Lana Abou Zeid, Albert Pell, Theo Tytus, Pascale Delangle, Carole Bresson
Summary: This study utilized HILIC-ESI-MS to separate multiphosphorylated cyclic peptides and their positional isomers, evaluating the selectivity of HILIC columns and the impact of mobile phase on separation selectivity. It explored the retention mechanism of different peptides, finding that the classic hydrophilic partitioning mechanism was followed exclusively on amide and diol columns. The research also revealed that the position of phosphorylated amino acids in the peptide backbone had an impact on retention, enabling the separation of positional isomers using HILIC.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Yi-En Liao, Jian Liu, Katelyn Arnold
Summary: Heparan sulfates and heparan sulfate binding proteins play crucial roles in regulating vascular homeostasis and host response in sepsis. Dysregulation of these molecules can exacerbate inflammation and coagulation. Understanding the structure-function relationship between heparan sulfates and heparan sulfate binding proteins is essential for drug development and potential therapeutic interventions in sepsis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Chemistry, Analytical
Fangling Wu, Liancheng Gu, Xinhua Dai, Shutong Yang, Fuxing Xu, Xiang Fang, Shaoning Yu, Chuan-Fan Ding
Summary: Positional isomer recognition is a challenging scientific issue, and the simultaneous recognition of ABSA isomers using TIMS-TOF-MS was achieved by measuring different ion mobility or spatial conformations. The study also demonstrated a method for relative quantification of the isomers with good linearity and precision at different molar ratios.
Article
Chemistry, Analytical
Jennifer L. Bonetti, Saer Samanipour, Arian C. van Asten
Summary: Differentiating positional isomers is a challenge for forensic laboratories, and a rapid and accurate identification method is needed. In this study, chemometric analysis of DART-ToF data was used, and the Random Forest algorithm was found to be efficient in distinguishing NPS positional ring isomers.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Miaomiao Li, Lars C. Pedersen, Ding Xu
Summary: Heparan sulfate-binding proteins (HSBPs) are structurally diverse extracellular and membrane attached proteins that interact with HS under normal physiological conditions. Interactions with HS offer an additional level of control over the localization and function of HSBPs. Manipulating HS-protein interactions could be explored as a therapeutic strategy to selectively antagonize/activate HSBPs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Chemistry, Analytical
Turaj Rahmani, Adriaan Ampe, Freideiric Lynen
Summary: This study evaluates the use of temperature-responsive and reversed-phase chiral liquid chromatography for enantioselective separation of a wide range of pharmaceutical compounds. Temperature-responsive liquid chromatography in the first dimension allows for analysis under purely aqueous conditions and complete refocusing of solutes prior to the second dimension. This enables the use of fast and broad compositional gradients over the chiral dimension, expanding the applicability of the technique.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Irina Dyukova, Ahmed Ben Faleh, Stephan Warnke, Natalia Yalovenko, Vasyl Yatsyna, Priyanka Bansal, Thomas R. Rizzo
Summary: Glycosylation patterns in monoclonal antibodies can vary significantly between different host cell types, affecting the safety, efficacy, and immunogenicity of the antibodies. This study demonstrates the potential of high-resolution ion mobility combined with cryogenic infrared spectroscopy in distinguishing isomeric glycans with different terminal galactose positions, which is critical for ensuring antibody quality. Additionally, the impact of host cell lines on the IgG G1F glycan profile at the isomer level was illustrated in this work.
Review
Spectroscopy
Mikael Fabritius, Baoru Yang
Summary: Analysis of triacylglycerol (TG) and phospholipid sn-positional isomers can be done through direct separation or quantification of regioisomer ratios using mass spectrometry. Direct chromatography separation is being replaced by mass spectrometry due to limitations. However, challenges arise from the large number of isobaric and isomeric lipid species in natural samples and the lack of available regiopure standards. Optimization algorithms and fragmentation models are useful for analysis of TG regioisomers.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Biochemical Research Methods
Tatsuyuki Kanamori, Yuki Okada, Hiroki Segawa, Tadashi Yamamuro, Kenji Kuwayama, Kenji Tsujikawa, Yuko T. Iwata
Summary: In this study, four synthetic opioids of benzimidazole and their four nitro group positional isomers were synthesized and analyzed. The results showed that the synthetic opioids had higher agonistic activity at the human mu-opioid receptors than fentanyl, while the isomers had lower activity. However, two of the isomers showed moderate activity similar to fentanyl.
DRUG TESTING AND ANALYSIS
(2023)
Article
Biochemical Research Methods
Salome Poyer, Ilham Seffouh, Chrystel Lopin-Bon, Jean-Claude Jacquinet, Jose L. Neira, Jean-Yves Salpin, Regis Daniel
Summary: The study developed a new analytical method for efficient differentiation and sensitive detection of different structures of chondroitin sulfate glycosaminoglycans, which was applied to analyze the disaccharide composition of biological reaction media.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
William E. Hackett, Joseph Zaia
Summary: The lack of consensus in glycoproteomics software and FDR estimation hinders the overlap of results, indicating a need for further research and improved methods for assessing overall results and FDR estimation performance.
Article
Biochemical Research Methods
Margaret Downs, Manveen K. Sethi, Rekha Raghunathan, Matthew D. Layne, Joseph Zaia
Summary: In this study, the matrisome proteins in Parkinson's disease (PD) were analyzed and significant differences were found in the expression of collagen proteins compared to control samples. Histological analysis supported these findings and showed similar trends in collagen abundance. The hydroxyprolination of collagen was less variable in PD compared to controls, and glycoproteomic changes were observed. Network topology-based analysis revealed the involvement of angiogenesis-related proteins in PD. Further studies with a larger cohort are needed to validate these results.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Mary Rachel Nalehua, Joseph Zaia
Summary: The biosynthetic enzymes in the secretory pathway create distributions of glycans at each glycosite that influence the biophysical properties and biological functions of glycoproteins. Understanding the heterogeneity of protein glycosylation is essential for quantifying changes in biological processes. Recent technical advances in mass spectral glycoproteomics analysis have improved our ability to accurately quantify these glycosylation changes.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Manveen K. Sethi, Margaret Downs, Chun Shao, William E. Hackett, Joanna J. Phillips, Joseph Zaia
Summary: This study investigates the glycosylation of extracellular matrix components in the development of Glioblastoma (GBM). The findings suggest that alterations in GAGs and PGs are closely related to GBM tumorigenesis. The study reveals significant differences in sulfation and glycosylation levels between GBM and control samples, as well as differential regulation of core matrisome proteins. These findings provide important insights into the molecular changes associated with GBM development.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
Gustavo J. Cavallero, Yan Wang, Charles Nwosu, Sheng Gu, Muthuraman Meiyappan, Joseph Zaia
Summary: Recombinant protein engineering design affects therapeutic properties including protein efficacy, safety, and immunogenicity. Glycosylation modulates glycoprotein therapeutic pharmacokinetics, pharmacodynamics, and effector functions. NanoHILIC-MS is advantageous in elucidating glycan features on glycotherapeutics that fail to be detected using traditional methods.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Deborah Chang, Joshua Klein, William E. Hackett, Mary Rachel Nalehua, Xiu-Feng Wan, Joseph Zaia
Summary: Glycosylation plays a critical role in the function and evolution of influenza A virus hemagglutinin (HA). The use of data-independent acquisition mass spectrometry allows for quantitative measurement of glycosylation changes and comparison between different viral expression systems and variants.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
Joseph Zaia
Summary: The 2022 Nobel Prize in Chemistry was awarded for the development of biorthogonal chemical ligation reactions, also known as click chemistry, in biomedicine. This concept has significantly advanced sensing and diagnosis, chemical biology, materials chemistry, and drug discovery and delivery. In the field of proteomics, the incorporation of click tags into proteins has revolutionized the selective enrichment of protein complexes and the study of protein networks, as well as the enrichment of protein post-translational modifications. This feature article summarizes the impact of biorthogonal click chemistry on proteomics.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Tin Long Wong, Brian P. Mooney, Gustavo J. Cavallero, Minhui Guan, Lei Li, Joseph Zaia, Xiu-Feng Wan
Summary: In this study, a glycoproteomic approach using the timsTOF Pro mass spectrometer was developed to analyze site-specific glycosylation in influenza glycoproteins. The method proved to be effective in quantifying glycopeptides and identifying low-abundance glycopeptides. The results showed variations in glycan types and quantities between different influenza viruses.
JOURNAL OF PROTEOME RESEARCH
(2023)
Editorial Material
Biochemical Research Methods
Shoumita Dasgupta, Joseph Zaia
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Editorial Material
Biochemical Research Methods
Joseph Zaia
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Juan Wei, Dimitris Papanastasiou, Mariangela Kosmopoulou, Athanasios Smyrnakis, Pengyu Hong, Nafisa Tursumamat, Joshua A. A. Klein, Chaoshuang Xia, Yang Tang, Joseph Zaia, Catherine E. E. Costello, Cheng Lin
Summary: Comprehensive de novo glycan sequencing is challenging due to the diversity and complexity of glycans. This study demonstrates the effectiveness of electron excitation dissociation (EED) mass spectrometry for glycan analysis, showing high sensitivity, fragmentation efficiency, and analysis speed. A novel EED MS2-guided MS3 approach is developed, allowing accurate determination of glycan topology and linkage configurations.
Article
Biochemistry & Molecular Biology
Guinevere S. M. Lageveen-Kammeijer, Erdmann Rapp, Deborah Chang, Pauline M. Rudd, Carsten Kettner, Joseph Zaia
Summary: The Minimum Information Required for a Glycomics Experiment (MIRAGE) is an initiative to standardize the reporting of glycoanalytical methods and to assess their reproducibility. They have published several reporting guidelines that describe the information that should be provided for glycoanalytical methods, and have now presented the first version of reporting guidelines for glyco(proteo)mics analysis by capillary electrophoresis (CE).