Article
Biochemical Research Methods
Kyle J. Juetten, Jennifer S. Brodbelt
Summary: The impact of supercharging on the fragmentation patterns of six proteins under denaturing conditions was investigated using five activation methods. Changes in sequence coverage, preferential cleavage sites, and fragment ion abundances were evaluated for each method. The results showed that supercharging had different effects on sequence coverage and preferential cleavage sites depending on the activation method and the protein.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
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
Simon K. Gammelgaard, Steffen B. Petersen, Kim F. Haselmann, Peter Kresten Nielsen
Summary: High-molecular weight products (HMWP) are critical quality attributes in insulin biopharmaceutical research and development. This study demonstrates the de novo characterization of cross-linked insulin dimers using top-down mass spectrometry workflows, including the efficient cleavage of interchain disulfide bonds and the identification of cross-link connectivities between chains. Various multistage approaches were utilized to identify the chemical composition and cross-link sites within the dimers, revealing specific cross-link patterns in different induced dimers.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Sean D. Dunham, Benqian Wei, Carter Lantz, Joseph A. Loo, Jennifer S. Brodbelt
Summary: 193 nm ultraviolet photodissociation (UVPD) allows high sequence coverage for intact proteins using terminal fragments alone. Internal fragments, which are usually ignored, have the potential to improve characterization of intact proteins. However, the identification of internal fragments generated by UVPD is less reproducible compared to HCD, with an increased risk of false-positive identifications. Proton-transfer charge reduction (PTCR) reactions can enhance the identification of internal fragments. Further research is needed to develop strategies to reduce false positive identifications of UVPD internal fragments.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Benqian Wei, Muhammad A. Zenaidee, Carter Lantz, Brad J. Williams, Sarah Totten, Rachel R. Ogorzalek Loo, Joseph A. Loo
Summary: This study demonstrates the benefits of analyzing internal fragments in improving the sequence coverage of disulfide-intact proteins, allowing for the determination of the position and connectivity of disulfide bonds. This is valuable for the characterization of biotherapeutic proteins.
Article
Chemistry, Analytical
Simon Becher, Huixin Wang, Michael G. Leeming, William A. Donald, Sven Heiles
Summary: UVPD is a powerful method in top-down proteomics, with sequence coverages exceeding those obtained with other fragmentation methods. Factors influencing protein fragmentation and sequence coverage are actively debated. The study on UVPD experiments on model proteins revealed that sequence coverage increases with higher charge states, and the presence of charge remote and charge directed fragmentation types depending on protonation sites and protein charge states.
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)
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
Chemistry, Analytical
Taran Driver, Vitali Averbukh, Leszek J. Frasinski, Jon P. Marangos, Marina Edelson-Averbukh
Summary: Two-dimensional partial covariance mass spectrometry (2D-PC-MS) utilizes fragment ion abundance fluctuations in tandem mass spectra to accurately identify intact protein ions, showing higher specificity and resolution compared to one-dimensional (1D) tandem mass spectrometry (MS/MS).
ANALYTICAL CHEMISTRY
(2021)
Article
Neurosciences
Jochem van Kempen, Marc A. Gieselmann, Michael Boyd, Nicholas A. Steinmetz, Tirin Moore, Tatiana A. Engel, Alexander Thiele
Summary: Fluctuations in cortical excitability affect sensory processing and behavior. These fluctuations are coordinated across different brain areas, with top-down attention enhancing this coordination. The degree of local state coordination between different areas can predict behavioral performance.
Article
Polymer Science
Aditi Khot, Brett M. Savoie
Summary: This study presents a coarse-grained modeling framework flexible enough to explore the structure-function relationships of organic mixed conductors exhibiting both ionic and electronic conductivity. The model successfully replicates experimental trends and reveals the complex interplay between polymer morphology, ionic-electronic coupling, and electrolyte distribution. This framework provides validation for future applications in establishing structure-function relationships in this important material class and suggests near-term opportunities for tailoring mixed conduction via side-chain design.
Article
Chemistry, Physical
Carles Navarro, Maciej Majewski, Gianni De Fabritiis
Summary: Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended time scales. This study presents a methodology that utilizes molecular dynamics simulations and neural networks to train a model that can accurately simulate protein folding events. The method eliminates the need for extensive simulations or labeled data and showcases extrapolation capabilities.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Yuan Qin, Xianfeng Zheng, Yu Song, Ge Sun, Jingsong Zhang
Summary: Photo-predissociation of rovibrational levels of SH(A(2)Sigma(+)) is studied, and the spin-orbit branching fractions of the products are measured to investigate the predissociation dynamics of different vibrational levels. It is found that the predissociation dynamics change drastically as the vibrational level increases.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Neurosciences
Adam Pines, Arielle S. Keller, Bart Larsen, Maxwell Bertolero, Arian Ashourvan, Dani S. Bassett, Matthew Cieslak, Sydney Covitz, Yong Fan, Eric Feczko, Audrey Houghton, Amanda R. Rueter, Manish Saggar, Golia Shafiei, Tinashe M. Tapera, Jacob Vogel, Sarah M. Weinstein, Russell T. Shinohara, Leanne M. Williams, Damien A. Fair, Theodore D. Satterthwaite
Summary: This study tracks cortical activity propagations using advanced neuroimaging and computer vision techniques in a large sample of youth (n = 388), showing that top-down cortical propagations become more prevalent with greater demands for cognitive control as well as with development in youth.
Article
Chemistry, Physical
Qian Liu, Zheng Li, Peng Liu, Wenshao Yang, Xueming Yang, Shengrui Yu
Summary: The spin-forbidden O(P-3(2)) + CO(X-1 sigma(+), v) channel formed from the photodissociation of CO2 in the low energy band centered at 148 nm is investigated. The vibrational-resolved images of the O(P-3(2)) photoproducts are analyzed to determine the TKER spectra, CO(X-1 sigma(+)) vibrational state distributions, and anisotropy parameters (beta). The results show the formation of correlated CO(X-1 sigma(+)) with specific vibrational bands and reveal a bimodal structure in the high vibrational bands.
JOURNAL OF CHEMICAL PHYSICS
(2023)