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
Chemistry, Analytical
Brock R. Juliano, Joseph W. Keating, Brandon T. Ruotolo
Summary: Membrane proteins are difficult to study using native top-down mass spectrometry due to the need for membrane mimetics. In this study, infrared photoactivation was explored as an alternative method for liberating membrane proteins from surfactant micelles. The results showed that infrared photoactivation can dissociate micelles composed of different detergent classes and can be extended to other membrane mimetics such as nanodiscs, liposomes, and bicelles. This technique significantly improves membrane protein sequence coverage, typically ranging from 40% to 60%.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Brock R. Juliano, Joseph W. Keating, Brandon T. Ruotolo
Summary: Membrane proteins are challenging targets for mass spectrometry due to the need for membrane mimetics. Infrared photoactivation has emerged as an alternative to liberate membrane proteins from surfactant micelles, but its mechanism and application in native proteomics are still unknown. This study evaluates and probes infrared photoactivation for membrane protein sequencing, proteoform identification, and native proteomics applications, and reveals its ability to dissociate detergent micelles and other membrane mimetics, as well as improve sequence coverage.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Qiao Zhang, Hsin Jung Tsai, Fuhua Li, Zhiming Wei, Qinye He, Jie Ding, Yuhang Liu, Zih-Yi Lin, Xiaoju Yang, Zhaoyang Chen, Fangxin Hu, Xuan Yang, Qing Tang, Hong Bin Yang, Sung-Fu Hung, Yueming Zhai
Summary: In this study, a Fe-P atom paired catalyst was constructed to accelerate the proton-coupled electron transfer (PCET) step and improve the catalytic activity of CO2-to-CO conversion. It was found that the P atom in the atom pair provided additional adsorption sites, accelerating water dissociation, boosting the hydrogenation of CO2, and enhancing the activity of CO2 reduction. This atom-pair catalytic strategy has the potential to overcome the inherent limitations of single-atom catalysts.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Optics
Kunlong Liu, Ingo Barth
Summary: This theoretical study examines the ionization enhancement of H-2(+) diatomic molecular ion using orthogonal two-color laser fields. The addition of a weak second-harmonic field is found to enhance ionization peaks at different critical internuclear distances. The analysis distinguishes two mechanisms underlying the enhanced ionization of H-2(+).
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
Nadine Prust, Pieter C. van Breugel, Simone Lemeer
Summary: This study reveals the significant roles of arginine phosphorylation in Bacillus subtilis and Staphylococcus aureus, highlights the challenges in large-scale analysis of protein phosphorylation, and proposes effective strategies and methods for overcoming these challenges. Additionally, it demonstrates the presence and impact of arginine phosphorylation in S. aureus through experimental validation.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Chemistry, Multidisciplinary
Darren T. Gass, Michael S. Cordes, Sebastian N. Alberti, H. Jamie Kim, Elyssia S. Gallagher
Summary: This study investigates ion/ion reactions using deuterium labeling and provides insights into the mechanisms of ion/ion and ion/molecule reactions for carbohydrates, which can improve the capability to differentiate complex biomolecules, such as carbohydrates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Analytical
Yang Mao, Shengjun Wang, Yuanqi Zhao, Andriana Konstantinidi, Lingyu Sun, Zilu Ye, Sergey Y. Vakhrushev
Summary: Comparison of different dissociation methods for O-glycopeptides showed that ETciD and EThcD outperformed HCD in terms of glycopeptide identification and site localization. Additionally, a pseudo-EThcD strategy combining electron transfer dissociation with paired HCD spectra demonstrated improvements in identification and quantification of isobaric mass tag-labeled O-glycopeptides, leading to the discovery of specific glycosites of GALNT11 in HepG2 cells.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
James D. Sanders, Samuel W. Shields, Edwin E. Escobar, Michael B. Lanzillotti, Jamie P. Butalewicz, Virginia K. James, Molly S. Blevins, Sarah N. Sipe, Jennifer S. Brodbelt
Summary: Researchers have developed a novel method that couples DTIMS with a UVPD-enabled Orbitrap mass spectrometer, enabling simultaneous localization of double bonds and accurate measurement of collision cross section for phospholipid isomers.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Milos Cejkov, Tyler Greer, Reid O'Brien Johnson, Xiaojing Zheng, Ning Li
Summary: Middle-down analysis using tandem mass spectrometry offers detailed insight into the primary structure of monoclonal antibodies with minimal sample preparation, by cleaving them into subunits for analysis. The design of experiments approach optimizes MS2 parameters, particularly those influencing ETD efficiency, to increase sequence coverage of antibody subunits. The DOE strategy enhances sequence coverage percentages utilizing only one fragmentation method, ETD, and can be extended to other advanced techniques for increased coverage.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Physical
Weijun Wu, Andrew E. E. Sifain, Courtney A. A. Delpo, Gregory D. D. Scholes
Summary: This study theoretically investigates the quantum dynamics of a donor-acceptor cavity system and finds that polaritons have the potential to enhance free charge carrier generation on an ultrafast timescale, but are suppressed by internal conversion and cavity loss on a longer timescale.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemical Research Methods
Corentin Beaumal, Evolene Desligniere, Helene Diemer, Christine Carapito, Sarah Cianferani, Oscar Hernandez-Alba
Summary: This study presents an improved method for the analysis of antibody-drug conjugates (ADCs) using dedicated software and proton transfer charge reduction. The method allows for a more comprehensive characterization and higher sequence coverage of ADCs, which is crucial for their development.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Anita O. Ducati, David Ruskic, Piotr Sosnowski, Takashi Baba, Ron Bonner, Gerard Hopfgartner
Summary: The study investigated CID and EID fragmentation mechanisms in LC-MS analysis, revealing that EID is superior to CID in generating specific and informative fragments for metabolite identification. EID also has the capability to provide structural information from adduct ions, offering the possibility for new metabolite characterization.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Analytical
Deepshikha Yadav, Shilpi Verma, Jyoti Choudhary, Harleen Kaur, Pratibha Tiwari, Sandeep Singh, Pallavi Kushwaha, Premshankar K. Dubey, Pranjal Chandra, Surinder P. Singh
Summary: In this study, an electrochemical biosensor based on AuNPs-MoS(2)NSs nanocomposite was developed for specific and rapid detection of FA. The sensor exhibited a low detection limit and good selectivity in the presence of interferents. It showed clinical potential in monitoring FA in human serum samples, demonstrating high reproducibility and stability.
Article
Biology
Tobias Moll, Valerie Odon, Calum Harvey, Mark O. Collins, Andrew Peden, John Franklin, Emily Graves, Jack N. G. Marshall, Cleide dos Santos Souza, Sai Zhang, Lydia Castelli, Guillaume Hautbergue, Mimoun Azzouz, David Gordon, Nevan Krogan, Laura Ferraiuolo, Michael P. Snyder, Pamela J. Shaw, Jan Rehwinkel, Johnathan Cooper-Knock
Summary: This study identifies a link between reduced expression of EXOSC2 and reduced SARS-CoV-2 replication. Increased expression of EXOSC2 is associated with higher risk of clinical COVID-19. The study also reveals interaction between the SARS-CoV-2 RNA polymerase and most of the human RNA exosome components.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemistry & Molecular Biology
Adam Frankish, Silvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet, Daniel Cerdan-Velez, Fiona Cunningham, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos Garcia Giron, Jose Manuel Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike Kay, Julien Lagarde, Fergal J. Martin, Laura Martinez Gomez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew Yates, Zahoor Zafrulla, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigo, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek
Summary: GENCODE provides high quality gene and transcript annotation for the human and mouse genomes, supported by experimental data, serving as a reference for genome biology and clinical genomics. The consortium generates data, develops tools and carries out analyses to support the identification and annotation of transcript structures and their function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Amelie Bonaud, Laetitia Gargowitsch, Simon M. Gilbert, Elanchezhian Rajan, Pablo Canales-Herrerias, Daniel Stockholm, Nabila F. Rahman, Mark O. Collins, Hakan Taskiran, Danika L. Hill, Andres Alloatti, Nagham Alouche, Stephanie Balor, Vanessa Soldan, Daniel Gillet, Julien Barbier, Francoise Bachelerie, Kenneth G. C. Smith, Julia Jellusova, Pierre Bruhns, Sebastian Amigorena, Karl Balabanian, Michelle A. Linterman, Andrew A. Peden, Marion Espeli
Summary: We identified SNARE Sec22b as a critical regulator of plasma cell maintenance and function. In the absence of Sec22b, plasma cells were hardly detectable and serum antibody titers were dramatically reduced, leading to a failure in mounting a protective immune response. Mechanistically, Sec22b contributes to efficient antibody secretion and is involved in regulating plasma cell transcriptional identity, as well as the morphology of the endoplasmic reticulum and mitochondria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Correction
Multidisciplinary Sciences
Marios G. G. Koliopoulos, Reyhan Muhammad, Theodoros I. Roumeliotis, Fabienne Beuron, Jyoti S. Choudhary, Claudio Alfieri
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Ian Jones, Lucas Dent, Tomoaki Higo, Theodoros Roumeliotis, Maria Arias Garcia, Hansa Shree, Jyoti Choudhary, Malin Pedersen, Chris Bakal
Summary: Almost all living cells maintain size uniformity through successive divisions. Proteins that over and underscale with size can act as rheostats, which regulate cell cycle progression. This study provides one of the first demonstrations of size-scaling phenomena in cancer and how morphology influences the chemistry of the cell.
Article
Biochemical Research Methods
Patrick Truong, Matthew The, Lukas Kall
Summary: A common goal in quantitative shotgun proteomics experiments is to identify proteins that show differential abundance under specific experimental conditions. However, this is challenging as mass spectrometry analyzes protein fragments rather than intact proteins. In this study, we demonstrate that a Bayesian hierarchical probabilistic model called Triqler can be adapted for data-independent acquisition (DIA) data after making minor changes to account for missing values. Furthermore, we show that Triqler outperforms other state-of-the-art protein summarization tools when evaluated on DIA data.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Siyu Wang, Louise Fairall, Trong Khoa Pham, Timothy J. Ragan, Dipti Vashi, Mark O. Collins, Cyril Dominguez, John W. R. Schwabe
Summary: This study reveals that MIER1 protein binds to both H2A:H2B histone dimer and complete histone octamer. Additionally, a larger MIER1:HDAC1:BAHD1:C1QBP complex co-purifies with an intact nucleosome containing di- or tri-methylated H3K27. These findings suggest that the MIER1 complex acts downstream of PRC2, expanding regions of repressed chromatin and potentially depositing histone octamer onto nucleosome-depleted regions of DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Mandy S. M. Wan, Reyhan Muhammad, Marios G. Koliopoulos, Theodoros I. Roumeliotis, Jyoti S. Choudhary, Claudio Alfieri
Summary: The study reveals the structure and mechanism of action of the SIN3B histone deacetylase. SIN3B stimulates catalysis by contacting the allosteric basic patch of the deacetylase and guides specific deacetylation through interaction with the substrate receptor subunit. These findings provide insights for future drug designs.
NATURE COMMUNICATIONS
(2023)
Article
Energy & Fuels
Rimjhim Yadav, Ayushi Saini, Jyoti Choudhary, Silki Sardana, Anil Ohlan, Kuldeep Singh, Surinder P. Singh
Summary: In this study, binary nanocomposites of PPy with MoS2 in two different morphologies were prepared. The PPyNTs/MoS2 nanocomposite exhibited higher specific capacitance and better cycling stability compared to PPyC/MoS2, making it a suitable electrode material for flexible supercapacitors.
Article
Biochemistry & Molecular Biology
Stephen J. Pettitt, Nan Shao, Diana Zatreanu, Jessica Frankum, Ilirjana Bajrami, Rachel Brough, Dragomir B. Krastev, Theodoros I. Roumeliotis, Jyoti S. Choudhary, Sonja Lorenz, Alistair Rust, Johann S. de Bono, Timothy A. Yap, Andrew N. J. Tutt, Christopher J. Lord
Summary: Reduced expression of HUWE1 leads to increased levels of BRCA1- increment 11q and PARPi resistance. This effect is specific to cells able to express BRCA1- increment 11q and is not seen in other BRCA1 or BRCA2 mutant cells. HUWE1 silencing also restores RAD51 nuclear foci and platinum salt resistance, indicating its potential as a biomarker for PARPi resistance in future clinical trials.
Article
Multidisciplinary Sciences
Jessica P. Burns, Christopher Wilding, Lukas Krasny, Xixuan Zhu, Madhumeeta Chadha, Yuen Bun Tam, P. S. H. Hari, Aswanth Mahalingam, Alexander T. J. Lee, Amani Arthur, Nafia Guljar, Emma Perkins, Valeriya Pankova, Andrew Jenks, Vanessa Djabatey, Cornelia Szecsei, Frank McCarthy, Chanthirika Ragulan, Martina I. Milighetti, Theodoros Roumeliotis, Stephen Crosier, Martina S. Finetti, Jyoti Choudhary, Ian Judson, Cyril F. Fisher, Eugene Schuster, Anguraj W. Sadanandam, Tom Chen, Daniel Williamson, Khin L. Thway, Robin Jones, Maggie C. U. H. Cheang, Paul Huang
Summary: This study conducted comprehensive proteomic profiling of tumor specimens from 321 STS patients and identified three proteomic subtypes within leiomyosarcomas with distinct myogenesis and immune features, anatomical site distribution and survival outcomes. The complement cascade is suggested as a candidate immunotherapeutic target for undifferentiated pleomorphic sarcomas and dedifferentiated liposarcomas. The study also defines functional signatures called Sarcoma Proteomic Modules that are independent prognostic factors for distant metastasis.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Mohamed Elghazaly, Mark O. Collins, Angela E. M. Ibler, Daniel Humphreys
Summary: Damage to our genome causes acute senescence in mammalian cells, which is a powerful tumor suppressor. Salmonella enterica hijacks this acute senescence to mediate intracellular infections. The study reveals the factors Wnt5a, INHBA, and GDF15 as necessary for acute senescence.
Meeting Abstract
Oncology
Phil Bland, Harry Saville, Abigail Read, Patty Wai, Gareth Muirhead, Lucinda Curnow, Jadwiga Nieminuszczy, Nivedita Ravindran, Marie John, Somaieh Hedayat, Holly Barker, James Wright, Lu Yu, Ioanna Mavrommati, Barrie Peck, Mark Allen, Patrycja Gazinska, Helen Pemberton, Aditi Gulati, Sarah Nash, Farzana Noor, Naomi Guppy, Ioannis Roxanis, Samantha Barlow, Helen Kalirai, Sarah Coupland, Ronan Broderick, Samar Alsafadi, Alexandre Houy, Marc-Henri Stern, Stephen Pettit, Jyoti Choudhary, Syed Haider, Wojciech Niedzwiedz, Christopher Lord, Rachael Natrajan
