Review
Biochemistry & Molecular Biology
Helisa H. Wippel, Juan D. Chavez, Xiaoting Tang, James E. Bruce
Summary: This article provides an overview of recent technological developments and applications of qXL-MS, including the design and synthesis of cross-linkers, development of new liquid chromatography-MS methodologies, and computational developments for data interpretation.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Zhen Chen, Junjie Chen
Summary: Proteins are crucial functional units that form complex networks which contribute to the proper functioning of cells and organisms. Advances in proteomics and mass spectrometry have enabled the identification of interacting proteins and the construction of comprehensive protein-protein interaction networks. These studies have been informative in investigating biological functions, particularly in the field of DNA damage response and repair.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2021)
Article
Biochemistry & Molecular Biology
Mihaela-Cristina Bunea, Victor-Constantin Diculescu, Monica Enculescu, Horia Iovu, Teodor Adrian Enache
Summary: The study investigated the electrochemical behavior and interaction of the immunosuppressive drug AZA with DNA. It was found that the reduction of AZA bound to the DNA layer induces structural changes and oxidative damage to the DNA double strands. This was confirmed through the occurrence of the oxidation peak of 8-oxo-deoxyguanosine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Applied
Jie Wang, Jie Liao, Honghai Wang, Xiaofang Zhu, Linqiu Li, Weibo Lu, Gongshuai Song, Qing Shen
Summary: A method for analyzing plasmalogens in shellfish was developed, with mussel identified as having the highest content and being a good choice for large-scale preparation.
Article
Biochemical Research Methods
Kenneth R. R. Durbin, Matthew T. T. Robey, Lilien N. N. Voong, Ryan T. T. Fellers, Corinne A. A. Lutomski, Tarick J. J. El-Baba, Carol V. V. Robinson, Neil L. L. Kelleher
Summary: Native mass spectrometry has become an important technique for determining the composition of protein complexes. However, there is a lack of software tools for comprehensive analysis of native mass spectrometry data. In this study, we introduce ProSight Native as an informatics platform that can determine the complete composition of protein complexes. We demonstrated its features by successfully determining the composition of a homotetrameric membrane complex and a heterodimer complex with associated ligands.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Alaa Riezk, Vasin Vasikasin, Richard C. C. Wilson, Timothy M. M. Rawson, James G. G. McLeod, Rishi Dhillon, Jamie Duckers, Anthony E. G. Cass, Alison H. H. Holmes
Summary: This study aimed to establish and validate a rapid and reliable liquid chromatography-tandem mass spectrometry (LC/MS) method for the simultaneous quantification of cefiderocol and meropenem in human plasma of critically ill patients. The method involved protein precipitation using acetonitrile for sample clean-up, followed by reverse phase chromatography using triple quadrupole LC/MS. The developed method showed good linearity, accuracy, and sensitivity for both cefiderocol and meropenem, with stability at different temperatures and protein binding assessed in human plasma.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Multidisciplinary
Eva Illes-Toth, Oliver J. Hale, James W. Hughes, Nicole Strittmatter, Jonathan Rose, Ben Clayton, Rebecca Sargeant, Stewart Jones, Andreas Dannhorn, Richard J. A. Goodwin, Helen J. Cooper
Summary: This study demonstrates for the first time the in situ mass spectrometry analysis of a non-covalent protein-drug complex formed in vivo, and provides a direct route for target-drug characterization in early stage drug discovery by spatial mapping across liver tissue.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Jing Chen, Qun Zhao, Hang Gao, Lili Zhao, Huiying Chu, Yichu Shan, Zhen Liang, Yukui Zhang, Lihua Zhang
Summary: Chemical cross-linking mass spectrometry (CXMS) is a powerful technology for analyzing protein complexes. However, in vivo CXMS studies have been limited by cross-linking biocompatibility and data analysis. In this study, a glycosidic bond-based MS-cleavable cross-linker called trehalose disuccinimidyl ester (TDS) was designed and synthesized, which simplified the cross-linked peptides into conventional single peptides via selective cleavage. TDS showed high biocompatibility and accuracy, enhancing the cross-linking identification accuracy and throughput.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Mohamed Sharafeldin, Felix Fleschhut, Timothy James, Jason J. Davis
Summary: The emergence of protein biomarkers promises a revolution in healthcare, shifting the focus from disease management to earlier intervention. This study introduces a convenient method for protein tagging prior to target capture, allowing for easy quantification of biomarkers. When translated to an automated microfluidic platform, the method enables rapid and accurate quantification of markers, showing good correlation with standard immunoassays. The platform is simple, versatile, highly sensitive, and does not require secondary labeling/binding or amplification.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Claudia Ctortecka, Karel Stejskal, Gabriela Krssakova, Sasha Mendjan, Karl Mechtler
Summary: Advancements in single-cell proteomics workflows have enhanced sensitivity and reproducibility for characterizing unknown biological phenomena. The introduction of multiplexed single-cell proteomics has led to a trend of combining single-cell measurements with abundant carriers to improve precursor selection and identification accuracy, although extreme carrier spikes may affect quantitative accuracy. Narrowly titrated carrier spikes have been found to provide comparable sensitivity with superior accuracy, while alternative multiplexing strategies can help evaluate data quality. Ultimately, optimized experimental designs for multiplexed proteomics of trace samples can lead to improved quantitative accuracy and elevated replicate overlap.
ANALYTICAL CHEMISTRY
(2022)
Review
Medicine, General & Internal
Chen-Xuan Wei, Michael Francis Burrow, Michael George Botelho, W. Keung Leung
Summary: Recent technological and analytical breakthroughs have enabled studies on small quantity, highly complex protein samples, such as salivary pellicle. Advances in mass spectrometry-based computational proteomics allow precise identification and quantification of complex protein samples, facilitating the determination of corresponding genes and cellular functions at the protein level through protein-protein interaction mapping. This has led to the breaking of barriers in research on small-quantity-complex-protein samples such as salivary pellicle.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Chemistry, Analytical
Chaoying Zhang, Zengnan Wu, Xinchang Gao, Xia Wang, Haifang Li, Jin-Ming Lin
Summary: This study proposes a noninterference ion addition (NIA) method by electrolysis to improve homogeneous crystallization during the evaporation process of sample droplets on the target plate, thus improving the quantitative detection of bacteria using MALDI-TOF MS. By inserting an active metal wire as the anode electrode in the droplet and releasing metal ions through electrolysis, the directional migration of metal ions under the electric field can hinder the migration of matrix molecules and homogenize the matrix crystals. Simultaneously, trace cationic surfactant is added to the droplet for pinning the contact surface to define the circular crystallization region. Metal ions from the anode electrode wire are deposited on the surface of the target plates, serving as the cathode, and do not interfere with ionization during MALDI-MS detection. This NIA method benefits homogeneous crystallization and improves quantitative analysis, making it suitable for biological samples with different matrices and allowing for quantitative analysis of bacterial samples.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Martijn M. Vanduijn, Hendrik-Jan Brouwer, Pablo Sanz de la Torre, Jean-Pierre Chervet, Theo M. Luider
Summary: The research team reported an improved electrochemical method that achieves complete reduction of both intermolecular and intramolecular disulfide bridges in a set of monoclonal antibodies. The method utilizes an online electrochemical flow cell to provide information on the pairing of heavy and light chains in the antibodies. The complete reduction of intramolecular disulfide bridges is important for the intact mass of the antibody chain and the confirmation of the protein's amino acid sequence.
ANALYTICAL CHEMISTRY
(2022)
Article
Virology
Jonas D. Albarnaz, Michael P. Weekes
Summary: The ability of host cells to detect and restrict viruses depends on a variety of cell-autonomous antiviral effectors and innate immune receptors. Proteomics is an ideal tool to understand the mechanisms of host antiviral immunity, as it allows for the analysis of changes in protein abundance, localization, modifications, and interactions. Furthermore, proteomics can provide insights into viral immune evasion strategies.
CURRENT OPINION IN VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mariela Gonzalez-Avendano, Simon Zuniga-Almonacid, Ian Silva, Boris Lavanderos, Felipe Robinson, Roberto Rosales-Rojas, Fabio Duran-Verdugo, Wendy Gonzalez, Monica Caceres, Oscar Cerda, Ariela Vergara-Jaque
Summary: The PPI-MASS web server provides an interactive platform for filtering protein sets based on biological features to identify protein-protein interactions with pharmacological potential. Users can manipulate filters to identify candidate proteins to establish physical contacts with a target protein, offering a powerful tool for the future design of associated therapies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Immunology
Anna Bujko, Nader Atlasy, Ole J. B. Landsverk, Lisa Richter, Sheraz Yaqub, Rune Horneland, Ole Oyen, Einar Martin Aandahl, Lars Aabakken, Hendrik G. Stunnenberg, Espen S. Baekkevold, Frode L. Jahnsen
JOURNAL OF EXPERIMENTAL MEDICINE
(2018)
Article
Oncology
A. E. Marneth, K. H. M. Prange, A. S. A. Al Hinai, S. M. Bergevoet, N. Tesi, E. M. Janssen-Megens, B. Kim, N. Sharifi, M. L. Yaspo, J. Kuster, M. A. Sanders, E. C. G. Stoetman, J. Knijnenburg, T. C. J. M. Arentsen-Peters, C. M. Zwaan, H. G. Stunnenberg, M. M. van den Heuvel-Eibrink, T. Haferlach, M. Fornerod, J. H. Jansen, P. J. M. Valk, B. A. van der Reijden, J. H. A. Martens
Correction
Oncology
C. Dell'Aversana, C. Giorgio, L. D'Amato, G. Lania, F. Matarese, S. Saeed, A. Di Costanzo, V. Belsito Petrizzi, C. Ingenito, J. H. A. Martens, I. Pallavicini, S. Minucci, A. Carissimo, H. G. Stunnenberg, L. Altucci
Article
Biochemistry & Molecular Biology
D. C. Ung, G. Iacono, H. Meziane, E. Blanchard, M-A Papon, M. Selten, J-R van Rhijn, R. Montjean, J. Rucci, S. Martin, A. Fleet, M-C Birling, S. Marouillat, R. Roepman, M. Selloum, A. Lux, R-A Thepault, P. Hamel, K. Mittal, J. B. Vincent, O. Dorseuil, H. G. Stunnenberg, P. Billuart, N. Nadif Kasri, Y. Herault, F. Laumonnier
MOLECULAR PSYCHIATRY
(2018)
Article
Genetics & Heredity
Dominik Glodzik, Sandro Morganella, Helen Davies, Peter T. Simpson, Yilong Li, Xueqing Zou, Javier Diez-Perez, Johan Staaf, Ludmil B. Alexandrov, Marcel Smid, Arie B. Brinkman, Inga Hansine Rye, Hege Russnes, Keiran Raine, Colin A. Purdie, Sunil R. Lakhani, Alastair M. Thompson, Ewan Birney, Hendrik G. Stunnenberg, Marc J. van de Vijver, John W. M. Martens, Anne-Lise Borresen-Dale, Andrea L. Richardson, Gu Kong, Alain Viari, Douglas Easton, Gerard Evan, Peter J. Campbell, Michael R. Stratton, Serena Nik-Zainal
Article
Cell & Tissue Engineering
Cristina D'Aniello, Ehsan Habibi, Federica Cermola, Debora Paris, Francesco Russo, Alessandro Fiorenzano, Gabriele Di Napoli, Dominique J. Melck, Gilda Cobellis, Claudia Angelini, Annalisa Fico, Robert Blelloch, Andrea Motta, Hendrik G. Stunnenberg, Dario De Cesare, Eduardo J. Patriarca, Gabriella Minchiotti
Article
Biochemistry & Molecular Biology
Siroon Bekkering, Rob J. W. Arts, Boris Novakovic, Ioannis Kourtzelis, Charlotte D. C. C. van der Heijden, Yang Li, Calin D. Popa, Rob ter Horst, Julia van Tuijl, Romana T. Netea-Maier, Frank L. van de Veerdonk, Triantafyllos Chavakis, Leo A. B. Joosten, Jos W. M. van der Meer, Henk Stunnenberg, Niels P. Riksen, Mihai G. Netea
Article
Microbiology
Rob J. W. Arts, Simone J. C. F. M. Moorlag, Boris Novakovic, Yang Li, Shuang-Yin Wang, Marije Oosting, Vinod Kumar, Ramnik J. Xavier, Cisca Wijmenga, Leo A. B. Joosten, Chantal B. E. M. Reusken, Christine S. Benn, Peter Aaby, Marion P. Koopmans, Hendrik G. Stunnenberg, Reinout van Crevel, Mihai G. Netea
CELL HOST & MICROBE
(2018)
Article
Endocrinology & Metabolism
Nadine C. Hornig, Pascal Rodens, Helmuth Doerr, Nina C. Hubner, Alexandra E. Kulle, Hans-Udo Schweikert, Maik Welzel, Susanne Bens, Olaf Hiort, Ralf Werner, Susanne Gonzalves, Anne Katrin Eckstein, Martine Cools, Annemarie Verrijn-Stuart, Hendrik G. Stunnenberg, Reiner Siebert, Ole Ammerpohl, Paul-Martin Holterhus
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2018)
Article
Multidisciplinary Sciences
Alessandro Bertero, Stephanie Brown, Pedro Madrigal, Anna Osnato, Daniel Ortmann, Loukia Yiangou, Juned Kadiwala, Nina C. Hubner, Igor Ruiz de los Mozos, Christoph Sadee, An-Sofie Lenaerts, Shota Nakanoh, Rodrigo Grandy, Edward Farnell, Jernej Ule, Hendrik G. Stunnenberg, Sasha Mendjan, Ludovic Vallier
Article
Cell Biology
Nunzio Del Gaudio, Antonella Di Costanzo, Ning Qing Liu, Lidio Conte, Antimo Migliaccio, Michiel Vermeulen, Joost H. A. Martens, Hendrik G. Stunnenberq, Angela Nebbioso, Lucia Altucci
CELL DEATH & DISEASE
(2019)
Article
Multidisciplinary Sciences
Yaser Atlasi, Seyed Mehdi Jafarnejad, Christos G. Gkogkas, Michiel Vermeulen, Nahum Sonenberg, Hendrik G. Stunnenberg
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Rene A. M. Dirks, Peter C. Thomas, Haoyu Wu, Robert C. Jones, Hendrik G. Stunnenberg, Hendrik Marks
Summary: The newly developed microfluidic PnP-ChIP-seq technology allows standardized and automated ChIP-seq analysis of low-input samples, providing a convenient method for researchers. This technology shows high-quality ChIP-seq results in various cells and can robustly detect epigenetic differences between different cellular states.
Article
Multidisciplinary Sciences
Nader Atlasy, Anna Bujko, Espen S. Baekkevold, Peter Brazda, Eva Janssen-Megens, Knut E. A. Lundin, Jorgen Jahnsen, Frode L. Jahnsen, Hendrik G. Stunnenberg
Summary: This study characterizes the immune cell compartment of the human small intestine during active Celiac disease using single cell transcriptomics. The results show altered myeloid cell transcriptomes and extensive changes in CD4(+) and CD8(+) T cell transcriptomes. In addition, a reduced population of natural intraepithelial lymphocytes is observed in Celiac disease.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Fatemeh Mirzadeh Azad, Eduard A. Struys, Victoria Wingert, Luciana Hannibal, Ken Mills, Joop H. Jansen, Daniel B. Longley, Hendrik G. Stunnenberg, Yaser Atlasi
Summary: Understanding the mechanisms of epigenetic regulation in ESCs is crucial for stem cell and developmental biology. In this study, the identification of Spic as a marker of ground state pluripotency and its role in controlling 1C metabolism and histone marks highlight the importance of auxiliary TFs in linking cellular metabolism to epigenetic regulation in ESCs.