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
Biotechnology & Applied Microbiology
Pavel Sinitcyn, Alicia L. Richards, Robert J. Weatheritt, Dain R. Brademan, Harald Marx, Evgenia Shishkova, Jesse G. Meyer, Alexander S. Hebert, Michael S. Westphall, Benjamin J. Blencowe, Juergen Cox, Joshua J. Coon
Summary: Deep proteome sequencing provides an 80% coverage of the human proteome. Shotgun proteomics experiments detect about 10,000 human proteins from a single sample, but fail to distinguish protein variants and isoforms. Our study using various methods identifies a million unique peptides and provides evidence for the translation of nonsynonymous variants.
NATURE BIOTECHNOLOGY
(2023)
Article
Chemistry, Analytical
Benqian Wei, Muhammad A. Zenaidee, Carter Lantz, Rachel R. Ogorzalek Loo, Joseph A. Loo
Summary: This study compares the fragmentation patterns of internal and terminal fragments in mass spectrometry and finds that they share similar fragmentation propensities. The formation of internal fragments can be explained by the mobile proton model, and they can combine with terminal fragments to form complementary product ions that span the entire protein sequence.
ANALYTICA CHIMICA ACTA
(2022)
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
Chemistry, Analytical
Runlong Cai, Wei Huang, Melissa Meder, Frederic Bourgain, Konstantin Aizikov, Matthieu Riva, Federico Bianchi, Mikael Ehn
Summary: By optimizing parameters, the sensitivity of CI-Orbitrap to trace gaseous compounds has been improved, extending the linear detection range, and applied in the measurement of oxygenated organic molecules in the atmosphere.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Runlong Cai, Wei Huang, Melissa Meder, Frederic Bourgain, Konstantin Aizikov, Matthieu Riva, Federico Bianchi, Mikael Ehn
Summary: In this study, the sensitivity of Q Exactive Orbitrap was improved by optimizing parameters, which resulted in a 50-fold increase in the detection range of trace compounds by CI-Orbitrap. The number of detected compounds in atmospheric measurements was significantly increased by improving the sensitivity.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Joseph S. Beckman, Valery G. Voinov, Michael Hare, Derrill Sturgeon, Yury Vasil'ev, Diana Oppenheimer, Jared B. Shaw, Shuai Wu, Rebecca Glaskin, Christian Klein, Cody Schwarzer, George Stafford
Summary: Electron-based dissociation (ExD) technology produces clean mass spectra for intact proteins and preserves labile post-translational modifications. By developing an efficient ExD cell and supporting software, current mass spectrometers can be retrofitted to allow for a wider range of protein analysis. ExD spectra can distinguish isobaric amino acids and preserve various post-translational modifications, enhancing the analytical certainty of characterizing peptides and proteins.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Plant Sciences
Sarah E. Flannery, Christopher Hepworth, William H. J. Wood, Federica Pastorelli, Christopher N. Hunter, Mark J. Dickman, Philip J. Jackson, Matthew P. Johnson
Summary: This study investigated the changes in thylakoid protein levels during long-term acclimation of Arabidopsis to different light intensities and found correlations with key photosynthetic parameters. High light promoted improved photosynthetic capacity and cyclic electron transport, while low light favored slowly reversible non-photochemical quenching. The data provide insights into how Arabidopsis tunes photosynthetic electron transfer and its regulation during developmental acclimation to light intensity.
Article
Engineering, Chemical
Jingyu Ren, Zhouzhou Yao, Qian Wei, Ruotong Wang, Yuan Liu, Long Wang, Kaibin Zheng, Shuai Wang, He Guo, Zhirui Niu, Jian Wang, Jin Han, Lei Lu, Yanzhong Zhen, Jie Li
Summary: In this study, representative organic pollutants in olive mill wastewater (OMW), ferulic acid (FA) and caffeic acid (CA), were effectively removed using dielectric barrier discharge (DBD) plasma and Mn/CoOOH/activated carbon fiber (ACF) catalyst. The electron transfer from the catalyst to O-3 and H2O2 promoted the dissociated adsorption, leading to the transformation of O-3 and H2O2 to reactive species. The possible degradation pathways of FA and CA were proposed.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Chemistry, Analytical
Neeleema Seetaloo, Monika Kish, Jonathan J. Phillips
Summary: Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) is a method for studying protein structures, which can be analyzed at different levels. However, the available software packages for HDX-MS data analysis can only handle different levels separately and lack the ability to combine them. Therefore, we developed a new standalone application (HDfleX) that allows the merging and analysis of HDX-MS data at different levels.
ANALYTICAL CHEMISTRY
(2022)
Article
Green & Sustainable Science & Technology
Gang Liu, Lei Liu, Yang Huo, Ziheng Dai, Liguo Zhang, Qilin Wang
Summary: This study improved the methane production in anaerobic digestion by combining FNA pretreatment and MnO2 addition. The activities of coenzyme F420 and ETS were increased in the two-phase AD model, indicating enhanced microbial metabolism. Furthermore, the enrichment of specific methanogens contributed to methane production.
JOURNAL OF CLEANER PRODUCTION
(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
Biochemical Research Methods
Weiyu Li, Chunyan Hou, Yaoxiang Li, Ci Wu, Junfeng Ma
Summary: Protein glycosylation is important for regulating biological processes, and mass spectrometry-based analysis is crucial for understanding these events. However, distinguishing structural isomers of glycans and glycopeptides remains challenging. In this study, a binary logistic regression model was established to classify O-GlcNAc/O-GalNAc peptides, achieving high accuracy (>87%). A corresponding web server, HexNAcQuest, was developed for easy integration in glycoproteomics workflows.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Multidisciplinary
Yuhang Liu, Jie Ding, Fuhua Li, Xiaozhi Su, Qitao Zhang, Guangjian Guan, Fangxin Hu, Jincheng Zhang, Qilun Wang, Yucheng Jiang, Bin Liu, Hong Bin Yang
Summary: Designing and synthesizing efficient and stable electrocatalysts is important for the hydrogen economy. Interfacial engineering is an effective strategy to optimize the kinetics of the hydrogen evolution reaction (HER) by inducing electron transfer. In this study, ultrafine RhP2/Rh nanoparticles embedded in N,P co-doped graphene were synthesized, and they exhibit outstanding HER performances under all pH conditions. The interfacial electron transfer from metallic Rh to semiconductive RhP2 enhances the HER kinetics, and activates the dual-site synergistic effect of Rh and P in neutral and alkaline environments, promoting faster HER kinetics.
ADVANCED MATERIALS
(2023)
Article
Materials Science, Multidisciplinary
Lei Wang, Ping Mu, Zixiang Zhou, Xin Zhang, Dezheng Liu, Ying Liang, Guijie Liang
Summary: In this study, a series of CdSe quantum dot-molecule complexes were assembled to investigate the triplet energy transfer process. The experimental results showed that the size of the quantum dots affects the rate of hole and electron transfer, but the transfer process is mainly determined by the energy level difference and wavefunction overlap.
RESULTS IN PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Louise Finch, Sarah Harris, Georgios Solomou, Jon Sen, Nikolaos Tzerakis, Richard D. Emes, Catherine S. Lane, Sarah R. Hart, Christopher F. Adams, Divya M. Chari
JOURNAL OF CONTROLLED RELEASE
(2020)
Article
Engineering, Chemical
Chuan Fu Yap, Manuel Garcia-Albornoz, Andrew F. Jarnuczak, Simon J. Hubbard, Jean-Marc Schwartz
Summary: Research has shown that under heat stress conditions, Saccharomyces cerevisiae increases trehalose production and glycolytic flux, with pyruvate kinase playing a key role in the increase in metabolic flux. The increase in trehalose metabolic pathway flux is primarily due to regulatory effects, and overexpression of enzymes involved in trehalose metabolism can lead to higher trehalose yield in the cell.
Article
Multidisciplinary Sciences
Fabian Morales-Polanco, Christian Bates, Jennifer Lui, Joseph Casson, Clara A. Solari, Mariavittoria Pizzinga, Gabriela Forte, Claire Griffin, Kirsten E. L. Garner, Harriet E. Burt, Hannah L. Dixon, Simon Hubbard, Paula Portela, Mark P. Ashe
Summary: Studies have shown that glycolytic mRNAs are localized to granules for active translation, which is critical for their localization and likely facilitates higher level organization and control of the glycolytic pathway. These granules, termed core fermentation (CoFe) granules, seem to function as translation factories for high-level coordinated enzyme synthesis necessary for a critical metabolic pathway.
Article
Cell Biology
Estefania Calvo-Alvarez, Serge Bonnefoy, Audrey Salles, Fiona E. Benson, Paul G. McKean, Philippe Bastin, Brice Rotureau
Summary: FLAM8 is not only a marker for flagellum length control in Trypanosoma brucei, but also reflects flagellum maturation in different parasite cycle stages, and even predicts daughter cell fate in specific tissue divisions.
CELLULAR MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Charlie F. Rowlands, Algy Taylor, Gillian Rice, Nicola Whiffin, Hildegard Nikki Hall, William G. Newman, Graeme C. M. Black, Raymond T. O'Keefe, Simon Hubbard, Andrew G. L. Douglas, Diana Baralle, Tracy A. Briggs, Jamie M. Ellingford
Summary: Variable gene expression levels between tissues complicate the use of RNA sequencing for delineating genomic variants impact. A gene and tissue-specific metric, MRSD, overcomes limitations of using expression values alone, estimating the required sequencing depth to achieve desired coverage. Fibroblasts are identified as the optimal RNA source using MRSD, demonstrating its utility in functional assessment of splicing aberrations, particularly in Mendelian genetic disorders context.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Christopher J. Kershaw, Michael G. Nelson, Jennifer Lui, Christian P. Bates, Martin D. Jennings, Simon J. Hubbard, Mark P. Ashe, Chris M. Grant
Summary: This study systematically determined the protein and mRNA composition of P-bodies and stress granules before and after nutrient stress, revealing the existence of high molecular weight complexes as potential seeds for mature condensates. Shared proteins and RNA components between these biological condensates were identified, highlighting a complex interaction profile during their maturation process. The interaction networks represent a tunable response to stress, showcasing previously unrecognized condensate heterogeneity.
Article
Biology
Robert A. Crawford, Mark P. Ashe, Simon J. Hubbard, Graham D. Pavitt
Summary: Translation regulation is an important cellular response to changing external conditions. This study identified RNA-binding proteins (RBPs) involved in translational control using polysome profiling and mass spectrometry. The results revealed previously under-appreciated RBPs and their roles in response to oxidative stress and amino acid starvation.
Article
Multidisciplinary Sciences
Mathias Walzer, David Garcia-Seisdedos, Ananth Prakash, Paul Brack, Peter Crowther, Robert L. Graham, Nancy George, Suhaib Mohammed, Pablo Moreno, Irene Papatheodorou, Simon J. Hubbard, Juan Antonio Vizcaino
Summary: This study introduces a re-analysis pipeline for public SWATH-MS datasets, which includes automated workflows and statistical analysis, and integrates the results into the Expression Atlas resource. By reanalysing 10 public DIA datasets, the robustness of the pipeline was validated, and the final results were integrated into Expression Atlas.
Review
Biochemistry & Molecular Biology
Declan R. Creamer, Simon J. Hubbard, Mark P. Ashe, Chris M. Grant
Summary: Eukaryotic cells have developed a complex circuitry of signalling molecules to monitor changes in their environments. The cAMP/PKA pathway is an important glucose sensing circuit in yeast, and PKA activity regulates various processes in yeast growth. However, the molecular basis of PKA signalling specificity is poorly understood.
Article
Biochemistry & Molecular Biology
Kwan Ting Kan, Michael G. Nelson, Chris M. Grant, Simon J. Hubbard, Hui Lu
Summary: Yme1 is a multifunctional protein that plays important roles in maintaining mitochondrial protein homeostasis and regulating biogenesis and function of mitochondrial proteins. This study shows that YME1 deletion affects yeast growth, chronological life span, mitochondrial protein homeostasis and function. It also reveals that Yme1 plays a key role in longevity and is important for maintaining the level and function of mitochondrial oxidative phosphorylation complexes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Martin Rusilowicz, David W. Newman, Declan R. Creamer, James Johnson, Kareena Adair, Victoria M. Harman, Chris M. Grant, Robert J. Beynon, Simon J. Hubbard
Summary: Protein quantitation via mass spectrometry requires the use of peptide proxies, and accurate quantitation often relies on the addition of an external standard. AlacatDesigner is a tool that assists in selecting suitable peptide candidates for recombinant protein standards. It considers factors such as target protein, existing databases, literature occurrence, potential post-translational modifications, and ionization potential within the mass spectrometer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jack Llewellyn, Venkatesh Mallikarjun, Ellen Appleton, Maria Osipova, Hamish T. J. Gilbert, Stephen M. Richardson, Simon J. Hubbard, Joe Swift
Summary: Cells respond to stress by producing chaperone proteins to maintain protein function, but aging leads to a disruption of protein balance and the formation of disease-related protein aggregates. Understanding the molecular causes of this proteostasis deterioration is important for disease interventions and cell health maintenance in regenerative medicine strategies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Immunology
James Edwards-Smallbone, Anders L. Jensen, Lydia E. Roberts, Francis Isidore G. Totanes, Sarah R. Hart, Catherine J. Merrick
Summary: A telomere-binding protein GBP2 has been identified in the early-diverging protozoan parasite Plasmodium, which can specifically bind to G-rich telomere repeats in quadruplex form and also bind to G-rich RNA. This protein is a multifunctional DNA/RNA-binding factor in Plasmodium.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Oncology
Neil Portman, Heloisa H. Milioli, Sarah Alexandrou, Rhiannon Coulson, Aliza Yong, Kristine J. Fernandez, Kee Ming Chia, Ensar Halilovic, Davendra Segara, Andrew Parker, Sue Haupt, Ygal Haupt, Wayne D. Tilley, Alex Swarbrick, C. Elizabeth Caldon, Elgene Lim
BREAST CANCER RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
M. Garcia-Albornoz, S. W. Holman, T. Antonisse, P. Daran-Lapujade, B. Teusink, R. J. Beynon, S. J. Hubbard