Article
Chemistry, Analytical
Samuel A. Miller, Kevin Jeanne Dit Fouque, Eldon R. Hard, Aaron T. Balana, Desmond Kaplan, Valery G. Voinov, Mark E. Ridgeway, Melvin A. Park, Gordon A. Anderson, Matthew R. Pratt, Francisco Fernandez-Lima
Summary: This study highlights the potential of using fast and high-resolution trapped ion mobility spectrometry combined with mass spectrometry to characterize alpha-synuclein positional glycoforms, offering insights for guiding therapeutic strategies for neurodegenerative disorders.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Francis Berthias, Hayden A. Thurman, Gayani Wijegunawardena, Haifan Wu, Alexandre A. Shvartsburg, Ole N. Jensen
Summary: Advances in proteomics have shown the ubiquity and biological importance of diverse proteoforms. The ability to separate and analyze intact isomeric proteoforms is crucial for understanding their functions. A novel technique using trapped IMS was demonstrated to achieve baseline resolution of isomeric proteoforms, opening new avenues in proteomics and epigenetics.
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
Chemistry, Analytical
Marek Polak, Michael Palasser, Alan Kadek, Daniel Kavan, Christopher A. Wootton, Marc-Andre Delsuc, Kathrin Breuker, Petr Novak, Maria A. van Agthoven
Summary: Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that uses modulation of precursor ion radii to show the fragmentation patterns of analytes. This study introduces quadrupolar detection in 2D MS and discusses its advantages, as well as adapts existing data processing techniques for accurate frequency-to-mass conversion. The method is applied to the top-down analysis of covalently labeled ubiquitin and the label-free relative quantification of biomolecule isoforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Muhammad A. Zenaidee, Benqian Wei, Carter Lantz, Hoi Ting Wu, Tyler R. Lambeth, Jolene K. Diedrich, Rachel R. Ogorzalek Loo, Ryan R. Julian, Joseph A. Loo
Summary: Analysis of internal fragments in TD-MS experiments can complement terminal fragments, increase protein sequence coverage, and enable more reliable localization of modification sites.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Carter Lantz, Muhammad A. Zenaidee, Benqian Wei, Zachary Hemminger, Rachel R. Ogorzalek Loo, Joseph A. Loo
Summary: ClipsMS is an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation, increasing sequence coverage for protein sequences. Internal fragments can enhance the information extracted from a single top-down mass spectrum.
JOURNAL OF PROTEOME RESEARCH
(2021)
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
Biochemical Research Methods
James M. Fulcher, Aman Makaju, Ronald J. Moore, Mowei Zhou, David A. Bennett, Philip L. De Jager, Wei-Jun Qian, Ljiljana Pasa-Tolic, Vladislav A. Petyuk
Summary: The study focused on how to improve the depth of top-down proteomics (TDP) using high-field asymmetric waveform ion mobility spectrometry (FAIMS), enhancing protein coverage in Alzheimer's disease brain tissue samples and identifying amyloid beta proteoforms associated with Alzheimer's disease.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Tanja Habeck, Frederik Lermyte
Summary: Top-down protein mass spectrometry provides valuable insights into protein sequence and structure, allowing for precise proteoform identification and the study of protein-ligand and protein-protein interactions. This method differs from traditional bottom-up approaches by analyzing intact proteins instead of digested peptides. This review provides an overview of top-down protein mass spectrometry experiments and highlights recent applications. Various experimental designs are recommended depending on whether sequence information or structural information is prioritized, as well as considerations of solution conditions and sample complexity.
ESSAYS IN BIOCHEMISTRY
(2023)
Article
Biochemical Research Methods
Michael Lanzillotti, Jennifer S. Brodbelt
Summary: This study compared the effects of 193 nm and 213 nm photons in ultraviolet photodissociation (UVPD) on 5 different proteins and evaluated the differences between the two wavelengths. The results showed that 213 nm UVPD more efficiently generated a specific type of fragment ions, possibly due to increased light absorption at the proline amide bond with 213 nm photons.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Multidisciplinary
Jan Leipert, Philipp T. Kaulich, Max K. Steinbach, Britta Steer, Konrad Winkels, Christine Blurton, Matthias Leippe, Andreas Tholey
Summary: Researchers have developed a sample preparation method based on protein aggregation and acidic elution, allowing for sensitive protein identification analysis of single nematodes on a digital microfluidics device. Compared to in-tube sample preparation, this method increases proteoform identifications by 46%. Label-free quantification also reveals changes in proteoform abundance that cannot be distinguished by bottom-up proteomics. This workflow facilitates proteoform-focused analysis on limited availability samples.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Rebecca L. Cain, Ian K. Webb
Summary: Electrospray ionization mass spectrometry (ESI-MS) experiments were used to study the solution-like structures of intact proteins, specifically by controlling the protein unfolding process and analyzing folding intermediates. By mixing various pH solutions online with aqueous cytochrome C, the changes in charge states, arrival time distributions (ATDs), and electron capture dissociation (ECD) were measured to detect folding intermediates and unfolded protein structures.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Ines C. Santos, Michael Lanzillotti, Ignat Shilov, Maria Basanta-Sanchez, Abhishek Roushan, Rose Lawler, Wilfred Tang, Marshall Bern, Jennifer S. Brodbelt
Summary: With the development of RNA-based therapeutics, the need for analytical methods to confirm sequences and map modifications has become urgent. This study compares different mass spectrometry techniques for sequencing modified nucleic acids and finds that UV photodissociation and activated electron photodetachment dissociation are effective for characterizing modified nucleic acids. However, different modifications can affect the fragmentation pathways and sequence coverage.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Analytical
Eleanor Watts, Ross Thyer, Andrew D. Ellington, Jennifer S. Brodbelt
Summary: With the rapid development of new biotherapeutics, it is crucial to ensure consistent quality and understand degradation pathways. This study presents a comprehensive mass spectrometry approach to analyze the sequences and structures of selenoproteins, as well as discover unknown by-products.
ANALYTICAL CHEMISTRY
(2022)
Article
Physics, Atomic, Molecular & Chemical
Melanie Cheung See Kit, Veronica V. Carvalho, Jonah Z. Vilseck, Ian K. Webb
Summary: Intramolecular interactions within a protein were studied using ion mobility-mass spectrometry (IM-MS), revealing structural changes in ubiquitin under different conditions through electrostatically reactive ion/ion chemistry and charge-based cross-linking. The identification of protonated sites in ubiquitin varied between solution conditions, indicating disruption of interactions maintaining the native protein structure. Gas-phase electrostatic cross-linking reagents supported similar structural changes, highlighting the role of solvent composition in determining protein conformation.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2021)
Article
Physics, Atomic, Molecular & Chemical
Dale A. Shepherd, Michael T. Marty, Kevin Giles, Andrew J. Baldwin, Justin L. P. Benesch
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2015)
Article
Biochemistry & Molecular Biology
Kris Holmes, Dale A. Shepherd, Alison E. Ashcroft, Mike Whelan, David J. Rowlands, Nicola J. Stonehouse
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Multidisciplinary Sciences
Georg K. A. Hochberg, Dale A. Shepherd, Erik G. Marklund, Indu Santhanagoplan, Matteo T. Degiacomi, Arthur Laganowsky, Timothy M. Allison, Eman Basha, Michael T. Marty, Martin R. Galpin, Weston B. Struwe, Andrew J. Baldwin, Elizabeth Vierling, Justin L. P. Benesch
Article
Biochemistry & Molecular Biology
Amit Sharma, Robert N. Leach, Christopher Gell, Nan Zhang, Patricia C. Burrows, Dale A. Shepherd, Sivaramesh Wigneshweraraj, David Alastair Smith, Xiaodong Zhang, Martin Buck, Peter G. Stockley, Roman Tuma
NUCLEIC ACIDS RESEARCH
(2014)
Article
Biochemistry & Molecular Biology
Indu Santhanagopalan, Matteo T. Degiacomi, Dale A. Shepherd, Georg K. A. Hochberg, Justin L. P. Benesch, Elizabeth Vierling
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biochemical Research Methods
Emmanuel Colson, Corentin Decroo, Dale Cooper-Shepherd, Guillaume Caulier, Celine Henoumont, Sophie Laurent, Julien De Winter, Patrick Flammang, Martin Palmer, Jan Claereboudt, Pascal Gerbaux
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2019)
Article
Biochemical Research Methods
Charles Eldrid, Aisha Ben-Younis, Jakub Ujma, Hannah Britt, Tristan Cragnolini, Symeon Kalfas, Dale Cooper-Shepherd, Nick Tomczyk, Kevin Giles, Mike Morris, Rehana Akter, Daniel Raleigh, Konstantinos Thalassinos
Summary: Ion mobility coupled to mass spectrometry (IM-MS) is widely utilized to study protein dynamics and structure in the gas phase. A high-resolution cyclic IM-mass spectrometer (cIM-MS) allows for multiple rounds of tandem IM experiments to be conducted, providing insights into protein unfolding pathways and dynamics. The IMn-MS technique shows evidence of interconversion between compact and extended protein structures, and suggests certain conformations have low energy barriers between them.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Evolene Desligniere, Thomas Botzanowski, Helene Diemer, Dale A. Cooper-Shepherd, Elsa Wagner-Rousset, Olivier Colas, Guillaume Bechade, Kevin Giles, Oscar Hernandez-Alba, Alain Bec, Sarah Cianferani
Summary: Monoclonal antibodies play a crucial role in treating cancer and immunological disorders, with disulfide bonds being key to the structure and activity of therapeutic antibodies. Monitoring disulfide connectivity and cysteine-related variants is essential during mAb manufacturing and storage, with mass spectrometry techniques being powerful tools for accurate identification of disulfide connectivity.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Katherine Gibson, Dale A. Cooper-Shepherd, Edward Pallister, Sophie E. Inman, Sophie E. Jackson, Viv Lindo
Summary: This study emphasizes the importance of evaluating interbatch purity and physical stability of therapeutic peptides. It highlights the difficulty in identifying isobaric impurities such as isoaspartic acid without synthesizing isoAsp peptide standards. The study demonstrates the value of cyclic ion mobility-mass spectrometry in determining the conformational characteristics of therapeutic peptides and locating isomerization sites.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Analytical
Dale A. Cooper-Shepherd, Hernando J. Olivos, Zhaoxiang Wu, Martin E. Palmer
Summary: The characterization of enantiomers is a significant challenge in chemical and life sciences. Evaluating the purity of chiral molecules is especially crucial in the pharmaceutical industry. This study utilizes the formation of dimers as diastereomeric pairs of enantiomers to separate them using high resolution cyclic ion mobility-mass spectrometry.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Julian A. Harrison, Adam Pruska, Philipp Bittner, Alexander Muck, Dale A. Cooper-Shepherd, Renato Zenobi
Summary: This study demonstrates the utilization of a new-generation high-resolution ion mobility instrument for the analysis of large biomolecular systems. The effects of voltages applied to different components of the cyclic ion mobility spectrometry system on ion transmission and arrival time distribution are investigated. The study also showcases the continuous monitoring of high-mass protein aggregation using a temperature-controlled electrospray ionization source coupled with the cyclic ion mobility mass spectrometer.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Dale A. Cooper-Shepherd, Jason Wildgoose, Boris Kozlov, William J. Johnson, Richard Tyldesley-Worster, Martin E. Palmer, John B. Hoyes, Michael McCullagh, Emrys Jones, Robert Tonge, Emma Marsden-Edwards, Peter Nixon, Anatoly Verenchikov, James I. Langridge
Summary: This article describes a new mass spectrometry system with a quadrupole-multireflecting time-of-flight design. The new multireflecting time-of-flight analyzer has a 48 m effective path length and uses planar, gridless ion mirrors, providing fourth-order energy focusing and achieving a resolving power over 200,000 fwhm and sub-ppm mass accuracy. We demonstrate how these attributes are maintained with relatively fast acquisition speeds, setting the system apart from other high resolution mass spectrometers. We have integrated this new system into both liquid chromatography-mass spectrometry and mass spectrometry imaging workflows to show the benefits of its instrument characteristics for these applications.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Andrej Kovac, Petra Majerova, Marianna Nytka, Monika Zajacova Cechova, Petr Bednar, Roman Hajek, Dale A. Cooper-Shepherd, Alexander Muck, Karel Lemr
Summary: Alzheimer's disease (AD) is a growing concern in neurodegenerative disorders. Aberrant forms of the protein tau, characterized by abnormal phosphorylation, are difficult to separate. The use of cyclic ion mobility-mass spectrometry offers a new method for analyzing these isomers in AD patient samples.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Dalton T. Snyder, Benjamin J. Jones, Yu-Fu Lin, Dale A. Cooper-Shepherd, Darren Hewitt, Jason Wildgoose, Jeffery M. Brown, James Langridge, Vicki H. Wysocki
Summary: This study describes the implementation of a simple three-electrode surface-induced dissociation (SID) cell on a cyclic ion mobility spectrometer (cIMS) and demonstrates the utility of multipass mobility separations for resolving multiple conformations of protein complexes. Multiple passes of intact complexes, or their SID fragments, increased the mobility resolution and were particularly useful for separating conformations produced from collision-induced and surface-induced unfolding experiments.