Article
Biochemistry & Molecular Biology
Mirela Sarbu, Raluca Ica, Edie Sharon, David E. Clemmer, Alina D. Zamfir
Summary: CS/DS play crucial roles in the extracellular matrix, and the structural analysis of their domains is essential; IMS MS technique can identify novel CS/DS species and provide important diagnostic fragment ions.
Article
Biotechnology & Applied Microbiology
Weijiao Zhang, Ruirui Xu, Xuerong Jin, Yang Wang, Litao Hu, Tianmeng Zhang, Guocheng Du, Zhen Kang
Summary: In this study, enzymatic strategies for producing homogeneous chondroitin oligosaccharides (o-CHs) and its sulfate derivatives from microbial sourced chondroitin were reported. The enzymatic approaches showed high conversion rates and pave the way for the study of structure-activity relationship and applications.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Danang Dwi Cahyadi, Munehiro Okamoto, Katsuhiko Warita, Naoko Takeda-Okuda, Jun-ichi Tamura, Yoshinao Z. Hosaka
Summary: The major disaccharide units of glycosaminoglycans (GAGs) in rhesus monkey tissues were found to be chondroitin sulfate (CS) and dermatan sulfate (DS), with the sulfation pattern primarily being of A and C types. Additionally, the E and iE types were specifically distributed in the tracheal and gastrointestinal tissues.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Review
Chemistry, Analytical
Yuelin Song, Qingqing Song, Wenjing Liu, Jun Li, Pengfei Tu
Summary: Currently, MS/MS is widely used in metabolomics for the identification of metabolites. However, the structural identification of isomers remains challenging due to the similarity of their MS/MS spectra. Differentiation and identification of isomers using MS/MS can be facilitated by various techniques, including chemical derivatization, ion mobility spectrometry, ion dissociation techniques, and energy-resolved MS. This tutorial provides a comprehensive summary of these cutting-edge techniques and emphasizes the importance of isomeric identification in metabolomics for analytical chemists. (c) 2023 Elsevier B.V. All rights reserved.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Applied
Lin Wei, Yingying Xu, Min Du, Ying Fan, Ruyi Zou, Xiangyu Xu, Qingdong Zhang, Yu-Zhong Zhang, Wenshuang Wang, Fuchuan Li
Summary: A novel 4-O-endosulfatase (endoBI4SF) was identified, which can efficiently remove 4-O-sulfated groups inside various CS/DS polysaccharides. This provides a much-needed tool to tailor the sulfation patterns and explore the related functions of 4-O-sulfated CS/DS chains.
CARBOHYDRATE POLYMERS
(2023)
Review
Chemistry, Analytical
Daniel G. Delafield, Gaoyuan Lu, Cameron J. Kaminsky, Lingjun Li
Summary: Mass spectrometry-based biomolecular analyses have become popular in research settings. Gas phase ion separation techniques provide a fourth dimension of analysis, enabling rapid characterization and high throughput profiling. This review highlights the latest developments and applications of high-end ion-mobility enabled instruments and their advantages for biomolecular research.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
David S. Roberts, Morgan Mann, Jake A. Melby, Eli J. Larson, Yanlong Zhu, Allan R. Brasier, Song Jin, Ying Ge
Summary: Researchers have successfully elucidated the complete structure of newly discovered O-glycans on the S protein regional-binding domain (SR-BD) of the SARS-CoV-2 virus through a hybrid mass spectrometry approach. This method can provide insights into the interactions between the virus and host cells, laying a foundation for understanding the functional roles of O-glycans in SARS-CoV-2 and other glycoproteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Applied
Minna Juvonen, Edwin Bakx, Henk Schols, Maija Tenkanen
Summary: This study investigated the potential of using TWIMS and CID-TWIMS-MS/MS to separate cereal-derived isomeric arabinoxylanoligosaccharides (A)XOS. The triand pentasaccharide isomers were distinguishable by the ATDs of the precursor ions, while CID-TWIMS-MS/MS could effectively separate isomeric fragment ions produced from tetra- and pentasaccharide (A)XOS. The base peak mobility spectrum was also introduced as a practical tool for (A)XOS fingerprinting.
Article
Chemistry, Analytical
Tyler S. Larson, Cameron D. Worthington, Matthew D. Verber, James E. Keating, Matthew R. Lockett, Gary L. Glish
Summary: The traditional data-dependent acquisition (DDA) approach for mass spectrometry selects precursor ions based on their absolute intensity, but may miss low-abundance species as biomarkers. This study proposes a new DDA approach called DiffN, which uses the relative differential intensity of ions between two samples to target species with large fold changes for analysis. The DiffN approach, coupled with a dual nano-electrospray (nESI) ionization source, showed promising results in quantifying lipid abundance differences in colorectal cancer cells.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Erpan Ahat, Yuefan Song, Ke Xia, Whitney Reid, Jie Li, Sarah Bui, Fuming Zhang, Robert J. Linhardt, Yanzhuang Wang
Summary: This study reveals that disrupting the Golgi structure affects the synthesis and secretion of glycosaminoglycans, leading to increased HS synthesis and decreased CS synthesis. The sulfation process of HS and CS is also altered in this case.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Yao Qian, Xiangyu Guo, Yunfang Wang, Zheng Ouyang, Xiaoxiao Ma
Summary: A mobility-modulated sequential dissociation (MMSD) strategy was developed for mass spectrometry imaging, enabling spatial lipidomics capable of multiplexed MS/MS imaging of 24 structurally distinct lipids. The method revealed a potential biomarker in a human hepatocellular carcinoma tissue.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biology
Lynn Kruger, Karina Biskup, Vasileios Karampelas, Antje Ludwig, Antje-Susanne Kasper, Wolfram C. Poller, Veronique Blanchard
Summary: In this study, an optimized strategy was presented to analyze glycosaminoglycan disaccharides via MALDI-TOF mass spectrometry, successfully identifying sulfation positions and patterns through fragmentation experiments.
Article
Biochemical Research Methods
Mirela Sarbu, Ligia Petrica, David E. Clemmer, Zeljka Vukelic, Alina D. Zamfir
Summary: GBM is a malignant and highly aggressive brain tumor with aberrant cell-surface glycosylation patterns in nearly all tumor cells. Profiling of ganglioside mixtures from GBM specimens revealed over 160 distinct components, dominated by GD3 and GT1 forms. The presence of GT1c(d18:1/24:1) was identified as a potential GBM marker for the first time using high performance ion mobility separation mass spectrometry.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
L. Edwin Gonzalez, Lucas J. Szalwinski, Thomas C. Sams, Eric T. Dziekonski, R. Graham Cooks
Summary: Lipidomic and metabolomic profiles of Bacillus subtilis and Bacillus thuringiensis were analyzed using two-dimensional tandem mass spectrometry, demonstrating the flexibility and informative power of this technique in rapid profiling screening for spore-forming biological agents.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Qingyu Hu, Yuting Sun, Xiyan Mu, Yulan Wang, Huiru Tang
Summary: Direct-infusion tandem mass spectrometry (DI-MS/MS) is valuable for quantitative metabolomics, MS imaging, and single cell studies, but cannot differentiate isomers/isobars with similar MS spectral features. In this study, the fragmentation pathways and characteristics of differential ion-mobility spectrometry (DMS) for four organic compounds were comprehensively investigated. A DI-DMS-MS/MS method was developed to simultaneously quantify these compounds. The method showed high accuracy and low limit-of-quantification, and clear differences between human and mouse urine samples were observed.
Article
Biochemical Research Methods
Ellen D. Inutan, Dean R. Jarois, Christopher B. Lietz, Tarick J. El-Baba, Efstathios A. Elia, Santosh Karki, Andjoe A. S. Sampat, Casey D. Foley, David E. Clemmer, Sarah Trimpin
Summary: By studying ubiquitin using IMS-MS with new ionization processes and different ion sources, researchers were able to compare mass-to-charge and drift time measurements for ubiquitin ions obtained through different ionization methods and found both similarities and differences in the structural features within the elongated distribution of structures. This suggests that the protein structures observed with ESI- or MAI-generated ions may not necessarily reflect the solution structures of the protein prior to ionization.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Calvin A. Austin, Ellen D. Inutan, Brian C. Bohrer, Jing Li, Joshua L. Fischer, Kanchana Wijerathne, Casey D. Foley, Christopher B. Lietz, Daniel W. Woodall, Lorelie F. Imperial, David E. Clemmer, Sarah Trimpin, Barbara S. Larsen
Summary: Ion mobility spectrometry mass spectrometry is able to separate differently branched multiply charged ions of star-branched poly(ethylene glycol) oligomers regardless of the ionization method used. The detailed structural characterization of isomers of the star-branched compositions was achieved using a home-built high-resolution ESI IMS-MS instrument. This approach allows for improved gas-phase separations and potential spatially resolved measurements compared to traditional ionization methods.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Daniel W. Woodall, Lucas W. Henderson, Shannon A. Raab, Kenji Honma, David E. Clemmer
Summary: The thermal denaturation of holomyoglobin in solution was characterized using ion mobility spectrometry and mass spectrometry techniques to investigate stability and structural changes. Two experimental approaches were utilized to induce thermal denaturation, highlighting the stabilizing effects of heme binding on the protein's stability.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Shannon A. Raab, Tarick J. El-, Daniel W. Woodall, Wen Liu, Yang Liu, Zane Baird, David A. Hales, Arthur Laganowsky, David H. Russell, David E. Clemmer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Editorial Material
Biochemical Research Methods
David H. Russell, David E. Clemmer
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Mirela Sarbu, Ligia Petrica, David E. Clemmer, Zeljka Vukelic, Alina D. Zamfir
Summary: GBM is a malignant and highly aggressive brain tumor with aberrant cell-surface glycosylation patterns in nearly all tumor cells. Profiling of ganglioside mixtures from GBM specimens revealed over 160 distinct components, dominated by GD3 and GT1 forms. The presence of GT1c(d18:1/24:1) was identified as a potential GBM marker for the first time using high performance ion mobility separation mass spectrometry.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Shannon A. Raab, Tarick J. El-Baba, Arthur Laganowsky, David H. Russell, Stephen J. Valentine, David E. Clemmer
Summary: The article discusses the impact of differences in time scales between protons and proteins on the conformation trapping during the electrospray process. It highlights the mechanisms of conformational changes and proton exchange at different time scales, as well as the immobilization of protons specific to protein conformations in the vacuum of the mass spectrometer.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemistry & Molecular Biology
Mirela Sarbu, Dragana Fabris, Zeljka Vukelic, David E. Clemmer, Alina D. Zamfir
Summary: Gangliosides play an important role in the central nervous system and can be used as diagnostic markers and potential therapeutic agents. Ion mobility separation mass spectrometry and IMS tandem mass spectrometry were used to study gangliosides in human central nervous system and cerebrospinal fluid. The results demonstrate the potential of IMS MS/MS in biomarker discovery and characterization, and its application in early diagnosis of CNS diseases through molecular fingerprints.
Article
Biochemical Research Methods
Zhi-chao Zhang, David A. Hales, David E. Clemmer
Summary: Diketopiperazine (DKP) formation is an important degradation pathway for peptides and proteins. The kinetics of peptide cleavage through DKP formation have been analyzed for different model peptides at multiple elevated temperatures. The results show that the degradation rate is influenced by the properties of the amino acid residues, with charged or polar side chains leading to faster degradation and nonpolar alkyl side chains providing stability. The stability of the peptides is influenced by various factors, including the presence of bulky groups on the alpha carbon and the preference for cis proline bond favored by the aromatic N-terminus.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Mirela Sarbu, Raluca Ica, Edie Sharon, David E. Clemmer, Alina D. Zamfir
Summary: CS/DS play crucial roles in the extracellular matrix, and the structural analysis of their domains is essential; IMS MS technique can identify novel CS/DS species and provide important diagnostic fragment ions.
Meeting Abstract
Biochemical Research Methods
Jonathan C. Trinidad, Xuyao Zeng, David E. Clemmer
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Xuyao Zeng, Milos Novotny, David E. Clemmer, Jonathan C. Trinidad
Summary: A substantial shortcoming of large-scale datasets is the difficulty in representing and visualizing key features, particularly in the study of glycopeptides and glycans. This paper presents a simple and concise graphical representation method to capture the microheterogeneity of glycan modification at specific sites, and provides visual illustrations of glycans and glycopeptides from various species.
Meeting Abstract
Biochemistry & Molecular Biology
M. Sarbu, Z. Vukelic, D. E. Clemmer, A. D. Zamfir
Article
Chemistry, Multidisciplinary
Santu Bera, Xuewei Dong, Bankala Krishnarjuna, Shannon A. Raab, David A. Hales, Wei Ji, Yiming Tang, Linda J. W. Shimon, Ayyalusamy Ramamoorthy, David E. Clemmer, Guanghong Wei, Ehud Gazit
Summary: This study explores the molecular basis behind the high solubility of the tripeptide Ala-Phe-Ala, demonstrating its unexpectedly high water solubility and unique structure. The research provides insight into the structural basis of solubility and offers a simple and feasible tool for estimation, with implications for peptide drug design, peptide materials, and advancing peptide nanotechnology.
CELL REPORTS PHYSICAL SCIENCE
(2021)