Article
Oncology
Marie-Eve Beaulieu, Sandra Martinez-Martin, Jastrinjan Kaur, Virginia Castillo Cano, Daniel Masso-Valles, Laia Foradada Felip, Sergio Lopez-Estevez, Erika Serrano del Pozo, Hugo Thabussot, Laura Soucek
Summary: The in vivo stability of therapeutic protein Omomyc was assessed in blood serum and tumor tissue. The results showed that the functional integrity of Omomyc remained preserved in the tumor tissue for at least 72 hours following administration and exhibited superior pharmacokinetics in the tumor compartment compared with blood serum. Therefore, Omomyc can be considered as an effective therapeutic agent.
Review
Biochemistry & Molecular Biology
Zheyi Liu, Xiong Chen, Shirui Yang, Ruijun Tian, Fangjun Wang
Summary: The discovery and understanding of functional protein complexes are crucial for the intervention in biological processes. The combination of affinity purification-mass spectrometry (AP-MS) and native top-down MS (nTDMS) has been developed to discover and analyze the structure of protein complexes. The integration of artificial intelligence (AI) with nTDMS can further enhance the investigation of functional protein complexes.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Applied
Hannah Mckerchar, Jolon M. Dyer, Juliet A. Gerrard, Evelyne Maes, Stefan Clerens, Renwick C. J. Dobson
Summary: The formation of lysinoalanine protein-protein crosslinks during food processing negatively affects nutritional value. However, directly mapping lysinoalanine in food is challenging. This study characterized the fragmentation pattern of lysinoalanine crosslinks in synthetic peptide models under different pH and time treatments using mass spectrometry. A potential diagnostic ion resulting from the cleavage of the α-carbon and β-carbon of lysinoalanine was identified, providing a more precise method for mapping lysinoalanine in real food samples compared to current software.
Article
Biochemical Research Methods
Li Chen, Wenyun Lu, Lin Wang, Xi Xing, Ziyang Chen, Xin Teng, Xianfeng Zeng, Antonio D. Muscarella, Yihui Shen, Alexis Cowan, Melanie R. McReynolds, Brandon J. Kennedy, Ashley M. Lato, Shawn R. Campagna, Mona Singh, Joshua D. Rabinowitz
Summary: NetID is a novel global network optimization approach for annotating untargeted LC-MS metabolomics data. By combining known biochemical and metabolomic principles, it significantly enhances annotation coverage and accuracy, facilitating the discovery of metabolites.
Article
Biochemistry & Molecular Biology
Guillaume Postic, Jessica Andreani, Julien Marcoux, Victor Reyss, Raphael Guerois, Julien Rey, Emmanuelle Mouton-Barbosa, Yves Vandenbrouck, Sarah Cianferani, Odile Burlet-Schiltz, Gilles Labesse, Pierre Tuffery
Summary: Proteo3Dnet is a web server dedicated to analyzing mass spectrometry interactomics experiments by searching for structurally interacting molecules, short linear motifs, and physically validated protein-protein interactions, providing a clearer overview of the data. The server returns a graph of identified interactions that can be interactively explored to understand core complexes and suggest undetected partners.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Pharmacology & Pharmacy
Francesco Fiorentino, Dante Rotili, Antonello Mai
Summary: Native mass spectrometry (nMS) is a biophysical method that allows the analysis of proteins in their native state, providing insights into protein complexes, protein-ligand interactions, and protein-protein interactions (PPIs). It has been increasingly used in early drug discovery for characterizing protein-drug interactions and evaluating PPI modulators. In this article, recent developments in nMS-directed drug discovery and potential applications of this technology in drug discovery are discussed.
DRUG DISCOVERY TODAY
(2023)
Review
Biochemistry & Molecular Biology
Hans H. Wandall, Mathias A. I. Nielsen, Sarah King-Smith, Noortje de Haan, Ieva Bagdonaite
Summary: O-glycosylation, particularly O-GalNAc glycans, plays crucial roles in tissue development, homeostasis, and host-microbe interactions. Technological advancements, such as mass spectrometry and genetic engineering, have allowed for a better understanding of O-glycosylation profiles and functions, with high-throughput O-glycoproteomics providing comprehensive insights. However, there is still much to explore, especially in understanding the context-dependent functions of O-glycans in different cellular processes and disease states.
Article
Multidisciplinary Sciences
Valeria Calvaresi, Antoni G. Wrobel, Joanna Toporowska, Dietmar Hammerschmid, Katie J. Doores, Richard T. Bradshaw, Ricardo B. Parsons, Donald J. Benton, Chloe Roustan, Eamonn Reading, Michael H. Malim, Steve J. Gamblin, Argyris Politis
Summary: In this study, the authors used hydrogen-deuterium exchange mass spectrometry to describe the evolution of the SARS-CoV-2 spike glycoprotein's structural dynamics features and receptor binding capability from the emergence of the original Wuhan isolate to the recent omicron variant. The findings shed light on the evolution of SARS-CoV-2 in the human population and the mechanisms of emergence of new variants.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Michael S. Westphall, Kenneth W. Lee, Colin Hemme, Austin Z. Salome, Keaton Mertz, Timothy Grant, Joshua J. Coon
Summary: This article describes an apparatus that can cryogenically land particles from the ion beam of a mass spectrometer onto transmission electron microscope grids for cryo-electron microscopy. This system also allows for the controlled formation of thin films of amorphous ice on the grid surface. The study demonstrates that using this cryogenic landing device significantly improves the structural preservation of deposited protein-protein complexes compared to room temperature landings, and landing under cryogenic conditions can increase the diversity of particle orientations, enabling improved 3D structural interpretation.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemical Research Methods
Haofeng Sun, Lingyun Ma, Leyu Wang, Peng Xiao, Hongmei Li, Min Zhou, Dewei Song
Summary: With the advancement of biomedical technology, protein epitope mapping has become crucial for developing and evaluating new protein drugs. The application of hydrogen-deuterium exchange for protein epitope mapping shows great potential, yet systematic reviews on this technology are limited. Despite some challenges, the technology offers significant advantages in research progress.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Jiechen Shen, Li Jia, Liuyi Dang, Yuanjie Su, Jie Zhang, Yintai Xu, Bojing Zhu, Zexuan Chen, Jingyu Wu, Rongxia Lan, Zhifang Hao, Chen Ma, Ting Zhao, Ni Gao, Jieyun Bai, Yuan Zhi, Jun Li, Junying Zhang, Shisheng Sun
Summary: This study introduces a modularization strategy and an algorithm named StrucGP for automated interpretation of N-glycan structures using tandem mass spectrometry, enabling detailed glycan structure determination on thousands of glycosites. The approach aids in identifying rare/new glycan structures and facilitates in-depth structural and functional study of glycoproteins in the biomedical research field. StrucGP offers a novel de novo glycan mapping method for determining detailed N-glycan structures at the site-specific level.
Article
Biochemical Research Methods
Jack Freestone, Temana Short, William Stafford Noble, Uri Keich
Summary: Target-decoy competition (TDC) is a commonly used method to control false discovery rate (FDR) in tandem mass spectrometry data analysis. However, the effectiveness of TDC depends on the homogeneity of the data. We developed Group-walk, a procedure that controls FDR in TDC by considering the group structure, leading to substantial power gains.
Review
Pharmacology & Pharmacy
Guodong Chen, Li Tao, Zhengjian Li
Summary: Molecular characterization of higher order structure in protein therapeutics is essential for various aspects in drug discovery and development. Recent advances in mass spectrometry offer orthogonal ways to characterize this structure and can be utilized for epitope mapping, aggregation assessment, and comparability studies. Future trends in applying these MS methods to HOS characterization are also discussed.
DRUG DISCOVERY TODAY
(2022)
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
Chemistry, Multidisciplinary
Yao Qian, Xiangyu Guo, Yunfang Wang, Zheng Ouyang, Xiaoxiao Ma
Summary: A mobility-modulated sequential dissociation (MMSD) strategy was developed for mass spectrometry imaging, enabling spatial lipidomics capable of multiplexed MS/MS imaging of 24 structurally distinct lipids. The method revealed a potential biomarker in a human hepatocellular carcinoma tissue.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemical Research Methods
Roxana E. Iacob, Stanley R. Krystek, Richard Y-C Huang, Hui Wei, Li Tao, Zheng Lin, Paul E. Morin, Michael L. Doyle, Adrienne A. Tymiak, John R. Engen, Guodong Chen
EXPERT REVIEW OF PROTEOMICS
(2015)
Article
Chemistry, Medicinal
Lumelle A. Schneeweis, Linda Obenauer-Kutner, Parminder Kaur, Aaron P. Yamniuk, James Tamura, Neil Jaffe, Brian W. O'Mara, Stuart Lindsay, Michael Doyle, James Bryson
JOURNAL OF PHARMACEUTICAL SCIENCES
(2015)
Article
Biochemical Research Methods
Vidhyashankar Ramamurthy, Aaron P. Yamniuk, Eric J. Lawrence, Wei Yong, Lumelle A. Schneeweis, Lin Cheng, Melissa Murdock, Martin J. Corbett, Michael L. Doyle, Steven Sheriff
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2015)
Article
Biochemical Research Methods
Patricia A. McDonnell, Joseph Yanchunas, John A. Newitt, Li Tao, Susan E. Kiefer, Marie Ortega, Stephanie Kut, Neil Burford, Valentina Goldfarb, Gerald J. Duke, Henry Shen, William Metzler, Michael Doyle, Zhong Chen, Christine Tarby, Robert Borzilleri, Wayne Vaccaro, Marco Gottardis, Songfeng Lu, Donald Crews, Kyoung Kim, Louis Lombardo, Deborah L. Roussell
ANALYTICAL BIOCHEMISTRY
(2009)
Article
Chemistry, Medicinal
Aaron P. Yamniuk, Noah Ditto, Mehul Patel, Jun Dai, Preeti Sejwal, Paul Stetsko, Michael L. Doyle
JOURNAL OF PHARMACEUTICAL SCIENCES
(2013)
Article
Pharmacology & Pharmacy
Ajit S. Narang, Aaron P. Yamniuk, Limin Zhang, S. Nilgun Comezoglu, Dilbir S. Bindra, Sailesh Varia, Michael L. Doyle, Sherif Badawy
JOURNAL OF PHARMACY AND PHARMACOLOGY
(2012)
Article
Biochemical Research Methods
Li Tao, Susan E. Kiefer, Dianlin Xie, James W. Bryson, Stanley A. Hefta, Michael L. Doyle
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2008)
Article
Biochemical Research Methods
Roxana E. Iacob, Guodong Chen, Joomi Ahn, Stephane Houel, Hui Wei, Jingjie Mo, Li Tao, Daniel Cohen, Dianlin Xie, Zheng Lin, Paul E. Morin, Michael L. Doyle, Adrienne A. Tymiak, John R. Engen
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2014)
Article
Medicine, Research & Experimental
Stuart L. Emanuel, Linda J. Engle, Ginger Chao, Rong-Rong Zhu, Carolyn Cao, Zheng Lin, Aaron Yamniuk, Jennifer Hosbach, Jennifer Brown, Elizabeth Fitzpatrick, Jochem Gokemeijer, Paul Morin, Brent Morse, Irvith M. Carvajal, David Fabrizio, Martin C. Wright, Ruchira Das Gupta, Michael Gosselin, Daniel Cataldo, Rolf P. Ryseck, Michael L. Doyle, Tai W. Wong, Raymond T. Camphausen, Sharon T. Cload, H. Nicholas Marsh, Marco M. Gottardis, Eric S. Furfine
Article
Biochemistry & Molecular Biology
KL Constantine, SR Krystek, MD Healy, ML Doyle, NO Siemers, J Thanassi, N Yan, DL Xie, V Goldfarb, J Yanchunas, L Tao, BA Dougherty, BT Farmer
Article
Immunology
Jenny H. Xie, Yifan Zhang, Martine Loubeau, Paul Mangan, Elizabeth Heimrich, Christian Tovar, Xiadi Zhou, Priyanka Madia, Michael Doyle, Shailesh Dudhgaonkar, Anjuman Rudra, Siva Subramani, James Young, Luisa Salter-Cid, Thomas R. Malek, Mary Struthers
Summary: Fusion protein of mouse IL-2 and CD25 shows promising therapeutic effects in treating SLE and diabetes without significant side effects.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Microbiology
J Yanchunas, DR Langley, L Tao, RE Rose, J Friborg, RJ Colonno, ML Doyle
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2005)
Article
Biochemistry & Molecular Biology
TE Carver, B Bordeau, MD Cummings, EC Petrella, MJ Pucci, LE Zawadzke, BA Dougherty, JA Tredup, JW Bryson, J Yanchunas, ML Doyle, MR Witmer, MI Nelen, RL DesJarlais, EP Jaeger, H Devine, ED Asel, BA Springer, R Bone, FR Salemme, MJ Todd
JOURNAL OF BIOLOGICAL CHEMISTRY
(2005)
Article
Biochemistry & Molecular Biology
ML Doyle, SS Tian, SG Miller, L Kessler, AE Baker, MR Brigham-Burke, SB Dillon, KJ Duffy, RM Keenan, R Lehr, J Rosen, LA Schneeweis, J Trill, PR Young, JI Luengo, P Lamb
JOURNAL OF BIOLOGICAL CHEMISTRY
(2003)
