Article
Chemistry, Medicinal
Samuel Cajahuaringa, Daniel L. Z. Caetano, Leandro N. N. Zanotto, Guido Araujo, Munir S. S. Skaf
Summary: Ion mobility mass spectrometry (IM-MS) techniques are valuable for structural characterization of biomolecular systems. However, interpreting IM-MS data is often challenging due to conformational isomerism. To address this, we developed MassCCS, an open-source code that computes the collision cross-section (CCS) of molecules using atomic and molecular buffer gas particles. MassCCS is highly accurate and efficient, especially for large macromolecular assemblies. Extensive tests showed its reliability, scalability, and performance. The code is freely available at https://github.com/cces-cepid/massccs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Optics
Ruti Ben-shlomi, Meirav Pinkas, Ziv Meir, Tomas Sikorsky, Or Katz, Nitzan Akerman, Roee Ozeri
Summary: A method for directly measuring atom-ion collisional cross section has been reported, with energy range of 0.2-12 mK x k(B) using ultracold atoms trapped in an optical-lattice and radio-frequency trapped ions to achieve high energy resolution. The energy resolution is estimated to be below 200 mu K x k(B) and the method allows for studying inelastic processes and searching for quantum signatures such as shape resonances.
Article
Biochemical Research Methods
Pearl Kwantwi-Barima, Christopher P. Harrilal, Sandilya V. B. Garimella, Isaac K. Attah, Richard D. Smith, Yehia M. Ibrahim
Summary: This study evaluated the effects of four different waveform profiles on collision cross section measurements using traveling wave ion mobility spectrometry. The results showed that the sawtooth waveform had lower measurement errors and better agreement with drift-tube-based measurements compared to the square waveform. However, the trend was opposite for steroids and nucleosides, suggesting different behavior for these molecules under ion heating conditions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Physics, Nuclear
Kristian Piscicchia, Magdalena Skurzok, Michael Cargnelli, Raffaele Del Grande, Laura Fabbietti, Johann Marton, Pawel Moskal, Angels Ramos, Alessandro Scordo, Diana Laura Sirghi, Oton Vazquez Doce, Johann Zmeskal, Slawomir Wycech, Paolo Branchini, Filippo Ceradini, Eryk Czerwinski, Erika De Lucia, Salvatore Fiore, Andrzej Kupsc, Giuseppe Mandaglio, Matteo Martini, Antonio Passeri, Vincenzo Patera, Elena Perez Del Rio, Andrea Selce, Michal Silarski, Catalina Curceanu
Summary: Simultaneous measurements of the cross sections for K- p -> Sigma(0)pi(0) and K- p -> Lambda pi(0) have been conducted using the kaon beam provided by the DA Phi NE collider. By detecting K- absorptions on hydrogen atoms in the gas mixture, the cross sections have been determined with the highest precision achieved so far in the low kaon momentum regime. These results impact pending questions in various fields, from nuclear and particle physics to astrophysics.
Review
Chemistry, Multidisciplinary
Emilia Christofi, Perdita Barran
Summary: The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology. An IM-MS workflow can provide mass, charge, and conformation information of a given target analyte, which is crucial for studying protein structures. This review focuses on the analysis of proteins and their complexes using IM-MS, discussing the typical features of an IM-MS experiment and how the data can be interpreted and compared with computational tools. The review also highlights the benefits of coupling mobility analysis to activation methods and its application to the study of conformationally dynamic and intrinsically disordered proteins.
Review
Biochemistry & Molecular Biology
Xiaohang Li, Hongda Wang, Meiting Jiang, Mengxiang Ding, Xiaoyan Xu, Bei Xu, Yadan Zou, Yuetong Yu, Wenzhi Yang
Summary: Ion mobility-mass spectrometry (IM-MS) is a powerful separation technique that enhances the separation and characterization of complex components. The integration of machine learning (ML) with IM-MS overcomes the lack of reference standards and helps in rapid, comprehensive, and accurate characterization of chemical components.
Review
Chemistry, Multidisciplinary
Jinan Wang, Pablo R. Arantes, Apurba Bhattarai, Rohaine V. Hsu, Shristi Pawnikar, Yu-ming M. Huang, Giulia Palermo, Yinglong Miao
Summary: Gaussian accelerated molecular dynamics (GaMD) is a robust computational method that accelerates biomolecular simulations by adding a harmonic boost potential, allowing for energetic reweighting via cumulant expansion to accurately reconstruct free energy landscapes. Hybrid schemes with other enhanced sampling methods have been introduced to further improve sampling and free energy calculations, enabling efficient characterization of biomolecular dynamics and interactions.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2021)
Article
Engineering, Environmental
Xue-Chao Song, Nicola Dreolin, Elena Canellas, Jeff Goshawk, Cristina Nerin
Summary: This study reports a method for predicting the collision cross-section (CCS) values, a structural descriptor, of extractables and leachables from plastic products using machine learning techniques. The model was developed by collecting experimental CCS values and assessing the performance of different molecular descriptors and machine learning algorithms. The results showed that a support vector machine (SVM) model based on Chemistry Development Kit (CDK) descriptors provided the most accurate prediction, which was successfully applied to the identification of plastic-related chemicals in river water.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Medicinal
Xue Wei, Wei-bo Cui, Gui-ya Qin, Xiu-e Zhang, Feng-yi Sun, Hui Li, Jing-fu Guo, Ai-min Ren
Summary: In this study, the photophysical properties of a series of Ru(II) complexes were investigated using density functional theory and time-dependent density functional theory methods. It was found that replacing methoxyls with pyrene groups greatly improved the lifetime of the complex, while adding acetylenyl groups subtly enhanced the two-photon absorption cross-section. These findings provide valuable theoretical guidance for the design and synthesis of efficient two-photon photosensitizers.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Materials Science, Multidisciplinary
Ming Lei, Sinisa Coh
Summary: In CrI3, an unusually large cross-polarized Raman signature of the A(g) phonon mode is observed, attributed to the combined effects of ferromagnetism on chromium atoms, spin-orbit interaction, and resonant effects. Surprisingly, the spin-orbit interaction potential is found to originate from iodine atoms, not chromium atoms where most of the magnetism lies. The Raman signature is analyzed with regards to magnetic order, magnetic moment direction, energy, light polarization, and carrier lifetime, revealing a strong phonon modulated magneto-optical Kerr effect in addition to the cross-polarized Raman signal.
PHYSICAL REVIEW MATERIALS
(2021)
Review
Chemistry, Multidisciplinary
Jon Paul Janet, Chenru Duan, Aditya Nandy, Fang Liu, Heather J. Kulik
Summary: The variability of chemical bonding in open-shell transition-metal complexes challenges conventional computational modeling tools. Tailoring ligand chemistry can alter preferred spin or oxidation states, creating vast regions of chemical space. Traditional DFT methods are limited in exploring transition-metal chemical space due to computational cost and inaccuracies.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biochemical Research Methods
Joon-Yong Lee, Aivett Bilbao, Christopher R. Conant, Kent J. Bloodsworth, Daniel J. Orton, Mowei Zhou, Jesse W. Wilson, Xueyun Zheng, Ian K. Webb, Ailin Li, Kim K. Hixson, John C. Fjeldsted, Yehia M. Ibrahim, Samuel H. Payne, Christer Jansson, Richard D. Smith, Thomas O. Metz
Summary: AutoCCS is an open-source software for rapid determination of CCS values from IMS-MS measurements, demonstrating accuracy and reproducibility for standard and unknown analyte ions under various conditions.
Article
Biochemistry & Molecular Biology
Fan Yang, Denice van Herwerden, Hugues Preud'homme, Saer Samanipour
Summary: High-resolution mass spectrometry combined with ion mobility spectrometry has been widely used in non-target screening, improving the accuracy of small molecule identification. Two CCS prediction models were developed using machine learning algorithm, successfully applied on different IMS platforms to eliminate false positives in small molecule identification.
Article
Materials Science, Multidisciplinary
Saber Gueddida, Fatma Aouaini, Sebastien Lebegue
Summary: In this study, the structural, electronic, and magnetic properties of tetranuclear molecular crystals were investigated using density functional theory. The calculated results successfully reproduced the two experimentally observed magnetic configurations, indicating ferromagnetic coupling between the magnetic centers.
JOURNAL OF MATERIALS RESEARCH AND TECHNOLOGY-JMR&T
(2022)
Article
Engineering, Electrical & Electronic
Rachel E. Jarvis, Justin G. Metcalf, Jay W. McDaniel
Summary: This article discusses a post-processing method to achieve highly accurate radar cross section (RCS) measurements in challenging test environments. By using the proposed stepped frequency continuous wave (SFCW) adaptive pulse compression (APC) algorithm, sidelobes of scatterers can be effectively suppressed, allowing for accurate RCS estimation.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2022)
Article
Chemistry, Multidisciplinary
Yun Zhu, Samantha Schrecke, Shuli Tang, Melanie T. Odenkirk, Thomas Walker, Lauren Stover, Jixing Lyu, Tianqi Zhang, David Russell, Erin S. Baker, Xin Yan, Arthur Laganowsky
Summary: This study reveals the selective modulation of phosphatidylserine (PS) binding to TRAAK by cupric ions, while TREK2 is unaffected. Other ions have no impact on the binding of both channels. Additionally, TRAAK shows stronger binding with Cu2+ and Zn2+ compared to TREK2.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Analytical
Thomas E. Walker, Arthur Laganowsky, David H. Russell
Summary: Charge reduction reactions play a crucial role in native mass spectrometry (nMS) by retaining native-like structures and noncovalent interactions of protein complexes. In this study, we provide new evidence that surface-active charge reducing reagents remove excess charge from droplets, thereby decreasing their overall charge. These processes are linked to the charge residue and ion evaporation models of electrospray ionization (ESI), and higher surface activity of amines leads to more efficient charge reduction of protein ions. Additionally, higher emitter potentials in ESI are associated with lower average charge states of protein complexes.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Kai S. Yang, Lauren R. Blankenship, Syuan-Ting Alex Kuo, Yan J. Sheng, Pingwei Li, Carol A. Fierke, David H. Russell, Xin Yan, Shiqing Xu, Wenshe Ray Liu
Summary: As a novel covalent modification, a Y-shaped, S-O-N-O-S-bridged post-translational cross-link connecting three residues C22, C44, and K61 in the main protease (M-Pro) of SARS-CoV-2 was frequently observed during crystallographic analyses. This cross-link potentially serves as a redox switch to regulate the catalytic activity of M-Pro, a drug target of COVID-19. Targeting the open active site formed by this linkage could be a potential strategy for the development of SARS-CoV-2 antivirals, especially in combination with other active-site-targeting molecules such as paxlovid.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Analytical
Varun V. Gadkari, Brock R. Juliano, Christopher S. Mallis, Jody C. May, Ruwan T. Kurulugama, John C. Fjeldsted, John A. McLean, David H. Russell, Brandon T. Ruotolo
Summary: Through comparing three laboratories, the reproducibility of collision-induced unfolding (CIU) in protein studies was evaluated. The results showed that within the same laboratory, CIU fingerprints were repeatable with an RMSD value of less than 5%. The collision cross section (CCS) values of CIU intermediates were consistent across the laboratories, but the activation potentials required for protein CIU transitions varied between the three laboratories.
Article
Chemistry, Analytical
Liqi Fan, David H. Russell
Summary: Cu, a highly redox active metal, can damage DNA and other cellular components, but its adverse effects can be mitigated by metallothioneins (MT). This study used mass spectrometry techniques to investigate the structure and stability of Cu-MT complexes and compared them with Ag-MT complexes. The results showed that Cu+ ions first bind to the beta-domain and then to the alpha-domain to form different Cu-i-MT complexes.
Article
Chemistry, Analytical
Robert L. Schrader, Thomas E. Walker, Sumeet Chakravorty, Gordon A. Anderson, Peter T. A. Reilly, David H. Russell
Summary: Digital mass filters are useful for analyzing large molecules as they can isolate high-m/z ions without requiring high RF and DC voltages. The Mathieu stability diagrams show that capacitors introduce voltage offsets between quadrupole rod pairs, depending on the waveform voltage and duty cycle. This changes the ion's a value, allowing for isolation of single-charge states for protein complexes up to 800 kDa. An isolation resolving power of approximately 280 was achieved for an ion of m/z 12,315 (z = 65+) for the 800.5 kDa GroEL D398A complex, corresponding to an m/z window of 44.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Cheng-Wei Lin, Shelby D. Oney-Hawthorne, Syuan-Ting Kuo, David P. Barondeau, David H. Russell
Summary: Iron-sulfur (Fe-S) cluster (ISC) cofactors are essential for many cellular processes. IscU plays a key role in the ISC Fe-S cluster biosynthetic pathway and exists in multiple conformational states. Zn binding affects the conformation of IscU and its interaction with IscS. This study provides a structural rationale for the role of Zn in stabilizing IscU conformations and IscS in preparing for cluster synthesis.
Article
Biochemical Research Methods
Dallas P. Freitas, Xi Chen, Erin A. Hirtzel, Madison E. Edwards, Joohan Kim, Hongying Wang, Yuxiang Sun, Klaudia I. Kocurek, David Russell, Xin Yan
Summary: In this study, we developed an in situ droplet-based derivatization method for rapid analysis of tissue lipids at multiple isomer levels. The method involves on-tissue derivatization using the TriVersa NanoMate LESA pipette, followed by extraction and analysis of the derivatized lipids using chip-based LESA mass spectrometry (MS) and tandem MS. This approach enables characterization of lipid isomers at the carbon-carbon double-bond positional and sn-positional levels, as well as relative quantitation based on diagnostic ion intensities. The method allows for multiple derivatizations at different spots in the same functional region of an organ, facilitating orthogonal lipid isomer analysis using a single tissue slide. Lipid isomers in different regions of the mouse brain were profiled, demonstrating the potential of this droplet-based derivatization method in tissue lipid studies requiring fast sample-to-result turnovers.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Dylan Ross, Aivett Bilbao, Joon-Yong Lee, Xueyun Zheng
Summary: We have developed mzapy, a Python package for efficient extraction and processing of mass spectrometry data, especially for complex data containing ion mobility spectrometry dimension. It includes supporting utilities for tasks such as calibration, signal processing, peak finding, and generating plots. The package is free and open-source and is structured to support future extensions to meet the evolving needs of the MS community.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Christopher P. Harrilal, Sandilya V. B. Garimella, Jaehun Chun, Nikhil Devanathan, Xueyun Zheng, Yehia M. Ibrahim, Carlos Larriba-Andaluz, Gregory Schenter, Richard D. Smith
Summary: The role of ion rotation in determining ion mobilities is explored using ion mobility spectrometry (IMS) measurements of isotopomer ions. Differences in ion mass distributions between isotopomer ions result in subtle ion mobility shifts which can be measured with high precision. The study investigates the rotational dependence of ion mobility shifts and finds that differences in rotational energy transfer during ion-molecule collisions contribute significantly to the separation of isotopomer ions. These findings demonstrate the potential of combining high-resolution IMS measurements with theory and computation for studying subtle structural differences between ions.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Lucas W. Henderson, Edie M. Sharon, Amit K. S. Gautam, Adam J. Anthony, Martin F. Jarrold, David H. Russell, Andreas Matouschek, David E. Clemmer
Summary: Mass spectrometry studies show that the stability of S. cerevisiae 20S proteasome undergoes related configurations and transitions during temperature changes, possibly linked to the opening of the proteolytic core. The study indicates that the proteasome remains intact and all transitions are reversible. Three types of structures are identified based on thermodynamic analysis: energetically stabilized closed configurations, high-entropy precursor states, and open pore structures. Opening of the 20S pore in the absence of the regulatory unit involves a charge-priming process. However, only a small fraction of precursor configurations actually open to expose the catalytic cavity.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemical Research Methods
Robert L. Schrader, Thomas E. Walker, David H. Russell
Summary: The use of mild collisional activation has been found to remove salts and adducts from large molecules, enhancing measurement accuracy and mass resolution. Adding a short square quadrupole between the ion funnel and transmission quadrupole effectively removes adducts and improves ejection efficiency for ions with low size-to-charge ratio.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Review
Biochemistry & Molecular Biology
Dylan H. Ross, Jian Guo, Aivett Bilbao, Tao Huan, Richard D. Smith, Xueyun Zheng
Summary: The identification of lipids is crucial in lipidomics studies, impacting the interpretation of analyses and biological understandings. Mass spectrometry coupled with liquid chromatography is commonly used for lipidomics studies, providing detailed lipid identifications. Ion mobility spectrometry has also gained adoption, offering additional separation dimension and supporting lipid identification. However, the availability of software tools for IMS-MS lipidomics data analysis is still limited, especially for isomer identifications and integration with MS-based imaging. This review evaluates existing software tools and lipid identifications in IMS-MS lipidomics data using open-access data from peer-reviewed literature.
Article
Chemistry, Multidisciplinary
Thomas Walker, He Mirabel Sun, Tiffany Gunnels, Vicki Wysocki, Arthur Laganowsky, Hays Rye, David Russell
Summary: Variable-temperature electrospray ionization (vT-ESI) native mass spectrometry (nMS) is used to investigate the thermodynamics of ATP binding to the GroEL tetradecamer chaperonin complex. The study reveals strong enthalpy-entropy compensation (EEC) and variations in stepwise free energy changes, which are consistent with the established nested cooperativity model of GroEL-ATP interactions. The entropy-driven ATP binding is attributed to ligand-induced conformational changes and reorganization of water molecules within the GroEL complex.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Dylan H. Ross, Joon-Yong Lee, Aivett Bilbao, Daniel J. Orton, Josie G. Eder, Meagan C. Burnet, Brooke L. Deatherage Kaiser, Jennifer E. Kyle, Xueyun Zheng
Summary: A Python tool called LipidOz was developed for the automated determination of lipid double bond positions from complex LC-OzID-IMS-MS data, using a combination of traditional automation and deep learning approaches. The development of this tool provides practical application for lipidomics research.
COMMUNICATIONS CHEMISTRY
(2023)
