Article
Biochemical Research Methods
Johanna Paris, Alina Theisen, Bryan P. Marzullo, Anisha Haris, Tomos E. Morgan, Mark P. Barrow, John O'Hara, Peter B. O'Connor
Summary: In this study, a variety of dissociation experiments were conducted on phosphopeptides using different fragmentation mechanisms in a mass spectrometer. The fragmentation patterns varied according to the composition of the peptides, with UVPD producing a large number of complementary fragments.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Analytical
Alina Theisen, Christopher A. Wootton, Anisha Haris, Tomos E. Morgan, Yuko P. Y. Lam, Mark P. Barrow, Peter B. O'Connor
Summary: In this study, 193 nm ultraviolet photodissociation (UVPD) was combined with 10.6 μm infrared multi-photon dissociation (IRMPD) to provide gentle slow-heating of UV-irradiated ions. The results showed that this method yielded high sequence coverage and increased fragmentation yield. Additionally, IR activation post UVPD further boosted the overall fragmentation yield and the intensity of specific fragments. UVPD was also implemented as a fragmentation method for 2DMS, demonstrating its viability.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Kim Steenbakkers, Aravindh N. Marimuthu, Britta Redlich, Gerrit C. Groenenboom, Sandra Bruenken
Summary: We present the first broadband vibrational action spectroscopic investigation of the linear radical cation of cyanoacetylene, HC3N+ ((2)pi), using the infrared pre-dissociation method. The vibronic splitting patterns of the bending modes were fully resolved, revealing previously unobserved bands. Spectroscopic constants obtained from the experimental data are in reasonable agreement with previous studies and ab initio calculations. The influence of the attached Ne atom on the infrared spectrum was also investigated.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Analytical
Kailin Zhang, Yingying Shi, Mengying Du, Yicheng Xu, Yan Wang, Xianglei Kong
Summary: Both infrared multiphoton dissociation (IRMPD) and ultraviolet photodissociation (UVPD) are crucial in tandem mass spectrometry and molecular spectroscopy, offering versatile ion activation choices. Integration of two tunable lasers with a Fourier transform ion cyclotron resonance mass spectrometer provides multiple capabilities for photon activation/dissociation experiments, including the ability to measure UVPD or IRMPD action spectra of fragment ions and demonstrate multistage tandem-in-time mass spectrometry performance up to MS4.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Kimberly Fabijanczuk, Zaikuan Josh Yu, Rose M. Bakestani, Rayan Murtada, Nicholas Denton, Kaylee Gaspar, Tara Otegui, Jose Acosta, Hilkka I. Kenttamaa, Henk Eshuis, Gao Jinshan
Summary: Inspired by the electron-activated dissociation technique, this study investigates the mechanisms of free radical-induced glycan dissociation using isotope labeling. Various fragment ions generated by one-step collisional activation, including cross-ring, glycosidic bond, and combinational cleavages, are accurately assigned and confirmed by mass difference of isotope labeling. The findings provide fundamental knowledge for interpreting complex free radical-induced glycan spectra and differentiating stereoisomers.
ANALYTICAL CHEMISTRY
(2023)
Article
Engineering, Environmental
C. F. Martins, L. A. Neves, R. Chagas, L. M. Ferreira, C. A. M. Afonso, I. M. Coelhoso, J. G. Crespo, J. PB. Mota
Summary: This study investigates the absorption of carbon dioxide (CO2) by ionic liquids (ILs) with quaternary ammonium cations combined with biocompatible anions from renewable sources. The research combines theoretical modeling and experimental analysis to understand the absorption characteristics and dynamics. Experimental validation of the proposed model provides insights for designing new absorption processes for CO2 capture.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Biochemical Research Methods
Chioma J. Akor, Carolyn J. Cassady
Summary: This study explores the use of in-source decay (ISD) and high-energy collision-induced dissociation (HE-CID) to provide structural information on alkali metal-adducted oligosaccharides. It is found that the matrix, the ionic radius of the metal ion used for adduction, and the affinity of metal ions for specific functional groups in the oligosaccharides all affect the ion production efficiency, product ion intensities, and the number of product ions formed in ISD and HE-CID. Different matrices also show varying effects on the dissociation of different types of oligosaccharides.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Gustavo J. Cavallero, Joseph Zaia
Summary: The combination of HILIC and cIM-MS proved to be an effective method for separating HS oligosaccharide isomers, including positional isomers and sulfate positions. This approach provides high-quality data for the discovery of new structural motifs for HS binding proteins and for targeted quality control analysis of commercial HS products.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Carter Lantz, Benqian Wei, Boyu Zhao, Wonhyeuk Jung, Andrew K. Goring, Jessie Le, Justin Miller, Rachel R. Ogorzalek Loo, Joseph A. Loo
Summary: Native mass spectrometry can provide information on the size and binding stoichiometry of proteins and protein assemblies, but determining their structures for understanding function is more difficult. Here, we show that fragmentation patterns from gas-phase protein complexes can provide higher-order structural information.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Dimitris Papanastasiou, Diamantis Kounadis, Alexandros Lekkas, Ioannis Orfanopoulos, Andreas Mpozatzidis, Athanasios Smyrnakis, Elias Panagiotopoulos, Mariangela Kosmopoulou, Maria Reinhardt-Szyba, Kyle Fort, Alexander Makarov, Roman A. Zubarev
Summary: This study successfully demonstrates multidimensional multiple-stage tandem processing of ions in a novel segmented linear ion trap. The trap incorporates various ion activation methods to provide enhanced performance. The results show that the fragmentation methods used in the Omnitrap platform can provide complete sequence coverage for partially unfolded ubiquitin. Furthermore, connecting the Omnitrap platform to an Orbitrap mass analyzer can further enhance performance.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Analytical
Bryan P. Marzullo, Tomos E. Morgan, Alina Theisen, Anisha Haris, Christopher A. Wootton, Simon J. Perry, Mansoor Saeed, Mark P. Barrow, Peter B. O'Connor
Summary: The study demonstrates the performance of the 193 nm UVPD fragmentation technique on structural/moiety characterization of agro-chemicals and shows its feasibility for these types of species. Using a 3D peak picking method, precursor specific fragments were successfully separated with milli-Dalton accuracy, achieving sub-part-per-million to part-per-billion mass accuracies across the entire 2DMS spectrum.
ANALYTICAL CHEMISTRY
(2021)
Article
Optics
Jeremy Xuan Yu Chew, Zi Heng Lim, Y. Qi, Guangcan Zhou, Guangya Zhou
Summary: Infrared devices are increasingly used in various applications. This paper introduces a novel dispersive spectrometer that has high-throughput and decoupled spectral resolution. The proposed spectrometer utilizes a two-stage Hadamard transform encoding process to increase the signal-to-noise ratio. With a single-pixel detector, the system can be easily implemented in other desired wavelengths. Additionally, a method is developed to remove the need for uniform illumination and improve the ease of device design for in situ measurement.
Article
Biochemical Research Methods
Takashi Baba, Khadijeh Rajabi, Suya Liu, Pavel Ryumin, Zoe Zhang, Kerstin Pohl, Jason Causon, J. C. Yves Le Blanc, Masaki Kurogochi
Summary: This study reports on the dissociation of singly protonated peptides using electron-activated dissociation (EAD). Two pathways, vibrational dissociation and radical-induced dissociation, were identified. The fast EAD device allows for additional molecular information and localization of modification groups.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Analytical
Shanshan Ma, Fangya Chen, Meng Zhang, Hang Yuan, Gangfeng Ouyang, Wuduo Zhao, Shusheng Zhang, Yufen Zhao
Summary: In this study, a sensitive method for glucose-containing disaccharide analysis was developed using mass spectrometry. The method was successfully applied to identify isomeric disaccharides in beers. The developed methodology is sensitive, fast, and reliable, providing a new approach for the structural analysis of oligosaccharides.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemical Research Methods
Fabien Hannauer, Rachelle Black, Andrew D. Ray, Eugen Stulz, G. John Langley, Stephen W. Holman
Summary: The fragmentation of oligonucleotides by mass spectrometry allows for sequence determination. Understanding the dissociation mechanisms of oligonucleotides in the gas phase enables the interpretation of data for obtaining sequence information. Recent studies have focused on the fragmentation of modified oligonucleotides, such as locked nucleic acids and modified nucleobases, which hold potential therapeutic interest.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Chemistry, Applied
Yanlei Yu, Fuming Zhang, Gina Renois-Predelus, I. Jonathan Amster, Robert J. Linhardt
CARBOHYDRATE POLYMERS
(2020)
Review
Biochemical Research Methods
Lauren E. Pepi, Patience Sanderson, Morgan Stickney, I. Jonathan Amster
Summary: This review discusses recent advancements in mass spectrometry (MS) for the analysis of glycosamino-glycans (GAGs). GAGs play key roles in various biological functions and have complex structural features, making their analysis challenging. However, improvements in MS techniques have significantly enhanced the precision and efficiency of structural characterization of GAGs.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Chemistry, Analytical
Danning Huang, Marcos Bouza, David A. Gaul, Franklin E. Leach, I. Jonathan Amster, Frank C. Schroeder, Arthur S. Edison, Facundo M. Fernandez
Summary: Fourier transform ion cyclotron resonance (FT-ICR) and Orbitrap mass spectrometry (MS) are high-performing analytical platforms in metabolomics, with high resolution and relative isotopic abundance measurements contributing to accurate metabolite annotation. Evaluations of Orbitrap ID-X and 12T solariX FT-ICR mass spectrometers show high mass accuracy and RIA measurements, aiding in the identification of correct elemental formulas for a wide range of metabolites. Overall, these FT-based MS platforms offer a systematic approach for metabolite annotation in biological systems, supporting the advancement of metabolomics research.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Lauren E. Pepi, Franklin E. Leach, Dustin R. Klein, Jennifer S. Brodbelt, I. Jonathan Amster
Summary: This study investigates the potential of UVPD in distinguishing chondroitin sulfate GAG epimers and the impact of experimental parameters on this differentiation. Results suggest that UVPD has promising capabilities in differentiating GAG structures, particularly in characterizing 4-O sulfation in CS-A GAGs.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemistry & Molecular Biology
Charlotte B. Spliid, Alejandro Gomez Toledo, Patience Sanderson, Yang Mao, Francesco Gatto, Tobias Gustavsson, Swati Choudhary, Ana L. Saldanha, Rasmus P. Vogelsang, Ismail Gogenur, Thor G. Theander, Franklin E. Leach, I. Jonathan Amster, Jeffrey D. Esko, Ali Salanti, Thomas Mandel Clausen
Summary: Placental malaria infection is mediated by the binding of the malarial VAR2CSA protein to chondroitin sulfate in the placenta, which has similarities to the structure found in cancer cells. The length and accessibility of chondroitin sulfate chains impact the binding of VAR2CSA and malaria infection. Upregulation of proteins involved in chondroitin polymerization in tumors suggests a role in selective tropism of VAR2CSA.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Editorial Material
Biochemical Research Methods
Lars Konermann, I. Jonathan Amster, Jeffrey C. Smith, Peter D. E. M. Verhaert
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Anjali Shenoy, Alexander R. Davis, Elijah T. Roberts, I. Jonathan Amster, Adam W. Barb
Summary: This study describes a novel yeast-based expression platform that simultaneously expresses the Kar2p chaperone and protein disulfide isomerase to facilitate the expression of secreted proteins. High-quality 15N-labeled human immunoglobulin fragments were successfully obtained by optimizing yeast expression conditions and developing a new growth medium. The interaction between the labeled immunoglobulin fragments and another protein was studied using NMR spectroscopy.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Multidisciplinary Sciences
Robert V. Williams, Chin Huang, Connor McDermott, Tanvir Ahmed, Linda Columbus, Kelley W. Moremen, James H. Prestegard, I. Jonathan Amster
Summary: This study demonstrates the kinetics of glycan addition by the OST-B enzyme and suggests that the order and efficiency of posttranslational glycosylation are influenced by steric cross-talk between adjoining acceptor sites. The findings provide insight into the function of these important enzymes and the site-specific recognition of glycosylation sequons by OST-B.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Robert Williams, Chin Huang, Kelley W. Moremen, I. Jonathan Amster, James H. Prestegard
Summary: The study reveals the importance of the interaction between hRobo1 and heparan sulfate (HS) for its biological activity. By introducing a lanthanide-binding peptide sequence, the researchers investigated the effect of HS binding on hRobo1. Through various experiments and analysis, it was found that the structure of hRobo1 undergoes slight changes and becomes more rigid upon HS binding, potentially affecting Robo-Slit signaling.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Nana Shao, Yu Fan, Chau-Wen Chou, Shadi Yavari, Robert Williams, I. Jonathan Amster, Stuart M. Brown, Ian J. Drake, Evert C. Duin, William B. Whitman, Yuchen Liu
Summary: This study presents an approach to study methyl-coenzyme M reductases (MCRs) from uncultured archaea by heterologous expression in a culturable methanogen, Methanococcus maripaludis. The results show that promoter, operon structure, and temperature are important factors for MCR production. Structural modeling suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Amanda O. Shaver, Brianna M. Garcia, Goncalo J. Gouveia, Alison M. Morse, Zihao Liu, Carter K. Asef, Ricardo M. Borges, Franklin E. Leach, Erik C. Andersen, I. Jonathan Amster, Facundo M. Fernandez, Arthur S. Edison, Lauren M. McIntyre
Summary: Untargeted metabolomics studies face challenges in identifying the same feature across studies. In this research, an anchored experimental design was developed, integrating three genetic studies of Caenorhabditis elegans. An anchor strain was included in every sample collection to estimate treatment effects within each batch and combine treatment effects across batches. This approach allows for comparison of stable spectral features across time without the need for compound identification.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Marissa L. L. Maciej-Hulme, Jasper J. J. Van Gemst, Patience Sanderson, Angelique L. W. M. M. Rops, Jo H. H. Berden, Bart Smeets, I. Jonathan Amster, Ton J. J. Rabelink, Johan van der Vlag
Summary: Proliferative forms of glomerulonephritis are characterized by leukocyte influx, albuminuria, and loss of kidney function. The glycocalyx, comprised of heparan sulfate, plays a crucial role in glomerular inflammation. Exogenous glomerular glycocalyx and low-molecular-weight heparin reduce proteinuria and granulocyte/macrophage influx in experimental glomerulonephritis, as well as prohibit granulocyte adhesion to glomerular endothelial cells. The development of HS-based therapeutics for inflammatory glomerular diseases is justified by these findings.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alexander R. Davis, Elijah T. Roberts, I. Jonathan Amster, Adam W. Barb
Summary: Despite the importance of glycoproteins in human biology, current methods for isotope labeling have limitations. This study presents a system using Saccharomyces cerevisiae for uniform labeling of IgG1, along with strategies to optimize expression yield. Two different media formulations were also developed, providing standardized and rich growth conditions.
JOURNAL OF BIOMOLECULAR NMR
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Robert Williams, Chin Huang, Kelley W. Moremen, I. Jonathan Amster, James H. Prestegard
Article
Biochemistry & Molecular Biology
Monique J. Rogals, Jeong-Yeh Yang, Robert Williams, Kelley W. Moremen, I. Jonathan Amster, James H. Prestegard
Summary: This study presents a relatively inexpensive and simple method to label all glycans plus all alanines of the highly glycosylated protein CEACAM1 by adding C-13-enriched glucose to standard commercial media. The approach allows for detection of partially occupied N-glycan sites, sites less susceptible to processing by an endoglycosidase, and unexpected truncation of the amino acid sequence. This labeling technique has potential applications in structural and functional screening of glycosylated proteins important to human health.
