Article
Biochemical Research Methods
Zach Rolfs, Lloyd M. Smith
Summary: A significant portion of unidentified fragment ion intensity in top-down proteomics is believed to come from internal fragment ions, which contain neither protein terminus. The computational complexity of internal fragment ions has historically limited their application to low-complexity samples, but the implementation of internal fragment ion functionality in MetaMorpheus allows for proteome-wide annotation of these ions, leading to disambiguation of proteoforms and increased identification accuracy. MetaMorpheus demonstrated success in disambiguating previously unclear proteoforms and improving proteoform-spectrum matches in mammalian cell lysates.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Muhammad A. Zenaidee, Benqian Wei, Carter Lantz, Hoi Ting Wu, Tyler R. Lambeth, Jolene K. Diedrich, Rachel R. Ogorzalek Loo, Ryan R. Julian, Joseph A. Loo
Summary: Analysis of internal fragments in TD-MS experiments can complement terminal fragments, increase protein sequence coverage, and enable more reliable localization of modification sites.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
Kyle A. Brown, Morgan K. Gugger, Zhen Yu, David Moreno, Song Jin, Ying Ge
Summary: Nonionic surfactants are commonly used reagents for cell lysis and protein extraction in structural biology. However, their presence often interferes with protein analysis by electrospray ionization-mass spectrometry (ESI-MS). This study introduces a cleavable surfactant, DSSM, which is compatible with ESI-MS analysis and enables top-down proteomics characterization. DSSM can replace DDM in proteomic experiments and structural biology studies.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Kyle A. Brown, Morgan K. Gugger, Zhen Yu, David Moreno, Song Jin, Ying Ge
Summary: Nonionic surfactants are widely used in cell lysis for protein extraction, stabilization, and purification in structural biology. However, they often interfere with electrospray ionization-mass spectrometry (ESI-MS) analysis. In this study, a cleavable nonionic surfactant, n-decyl-disulfide-beta-D-maltoside (DSSM), was developed to overcome this limitation. DSSM is compatible with ESI-MS and reversed-phase liquid chromatography-MS analysis and allows for characterization of membrane proteins and endogenous proteins, making it a potential replacement for the commonly used surfactant DDM in proteomic experiments and structural biology studies.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Carter Lantz, Muhammad A. Zenaidee, Benqian Wei, Zachary Hemminger, Rachel R. Ogorzalek Loo, Joseph A. Loo
Summary: ClipsMS is an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation, increasing sequence coverage for protein sequences. Internal fragments can enhance the information extracted from a single top-down mass spectrum.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Analytical
Sule Yilmaz, Florian Busch, Nagarjuna Nagaraj, Juergen Cox
Summary: Researchers have developed a novel computational proteomics workflow called MaxLynx for analyzing cross-linking combined with mass spectrometry (XL-MS) data, which has shown better performance in testing.
ANALYTICAL CHEMISTRY
(2022)
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
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
Fanny C. Liu, Samuel R. Kirk, Kirsten A. Caldwell, Thais Pedrete, Florian Meier, Christian Bleiholder
Summary: Top-down proteomics is a challenging but direct approach to studying proteoforms. This study utilizes ion mobility spectrometry/mass spectrometry (IMS/MS) to separate top-down fragment ions and reveals that these ions exhibit multiple stable conformations influenced by their amino acid sequence. The study also suggests that the folding process of fragment ions can lead to kinetic trapping of intermediate states in ion mobility measurements.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Thomas Kenderdine, William Mcintyre, Ghazaleh Yassaghi, Daniele Rollo, Alexander Bunkowski, Lukas Goerlach, Detlev Suckau, Guillaume Tremintin, Michael Greig, Christopher Bell, Daniele Fabris
Summary: In this report, the behavior of oligoribonucleotide samples ranging from 20 to 364 nt upon collision-induced dissociation (CID) was examined. The experimental data showed a progressive shift from terminal to internal fragments as a function of size. Simulation results highlighted the ability of internal fragments to produce self-consistent ladders, which enabled proper alignment and recognition of the nucleotides. The combination of information from internal and terminal fragments resulted in a greater sequence coverage and nucleotide coverage depth.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Review
Biochemical Research Methods
Jiancheng Zhong, Yusui Sun, Minzhu Xie, Wei Peng, Chushu Zhang, Fang-Xiang Wu, Jianxin Wang
Summary: Proteins play a crucial role in living processes, and changes in their molecular structure are closely tied to disease pathology. Mass spectrometry enables the characterization of proteoforms, but faces various challenges that require the use of different methods and algorithms for optimization.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Analytical
Francis Berthias, Hayden A. Thurman, Gayani Wijegunawardena, Haifan Wu, Alexandre A. Shvartsburg, Ole N. Jensen
Summary: Advances in proteomics have shown the ubiquity and biological importance of diverse proteoforms. The ability to separate and analyze intact isomeric proteoforms is crucial for understanding their functions. A novel technique using trapped IMS was demonstrated to achieve baseline resolution of isomeric proteoforms, opening new avenues in proteomics and epigenetics.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Corinne A. Lutomski, Tarick J. El-Baba, Joshua D. Hinkle, Idlir Liko, Jack L. Bennett, Neha V. Kalmankar, Andrew Dolan, Carla Kirschbaum, Kim Greis, Leonhard H. Urner, Parth Kapoor, Hsin-Yung Yen, Kevin Pagel, Christopher Mullen, John E. P. Syka, Carol V. Robinson
Summary: By using an infrared laser in a high-pressure linear ion trap, researchers were able to remove detergent micelles and obtain good sequence coverage for membrane proteins and their complexes through top-down mass spectrometry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Samuel A. Miller, Kevin Jeanne Dit Fouque, Eldon R. Hard, Aaron T. Balana, Desmond Kaplan, Valery G. Voinov, Mark E. Ridgeway, Melvin A. Park, Gordon A. Anderson, Matthew R. Pratt, Francisco Fernandez-Lima
Summary: This study highlights the potential of using fast and high-resolution trapped ion mobility spectrometry combined with mass spectrometry to characterize alpha-synuclein positional glycoforms, offering insights for guiding therapeutic strategies for neurodegenerative disorders.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Whitaker Cohn, Romain Huguet, Vlad Zabrouskov, Julian Whitelegge
Summary: Membrane proteins with transmembrane α-helical domains tend to retain structure in the gas phase, posing challenges for efficient electron capture/transfer dissociation in top-down MS. In this study, comparison of different dissociation modes on a modern Orbitrap platform for a model membrane protein showed that HCD outperformed CAD and ETD. A combination of ETD and HCD (EThcD) demonstrated significant synergy over using HCD or ETD alone, offering potential similar to activated ion electron capture dissociation. UV photodissociation at 213 nm displayed multiple backbone dissociation mechanisms, covering almost all backbone bonds, indicating high potential for this technique.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Oncology
Elizabeth C. Randall, Begona G. C. Lopez, Sen Peng, Michael S. Regan, Walid M. Abdelmoula, Sankha S. Basu, Sandro Santagata, Haejin Yoon, Marcia C. Haigis, Jeffrey N. Agar, Nhan L. Tran, William F. Elmquist, Forest M. White, Jann N. Sarkaria, Nathalie Y. R. Agar
Article
Cell Biology
Yagmur Micoogullari, Sankha S. Basu, Jessie Ang, Nina Weisshaar, Nicholas D. Schmitt, Walid M. Abdelmoula, Begona Lopez, Jeffrey N. Agar, Nathalie Agar, John Hanna
MOLECULAR BIOLOGY OF THE CELL
(2020)
Article
Multidisciplinary Sciences
Krishna C. Aluri, Joseph P. Salisbury, Jochen H. M. Prehn, Jeffrey N. Agar
SCIENTIFIC REPORTS
(2020)
Article
Biochemical Research Methods
Kristina Srzentic, Luca Fornelli, Yury O. Tsybin, Joseph A. Loo, Henrique Seckler, Jeffrey N. Agar, Lissa C. Anderson, Dina L. Bai, Alain Beck, Jennifer S. Brodbelt, Yuri E. M. van der Burgt, Julia Chamot-Rooke, Sneha Chatterjee, Yunqiu Chen, David J. Clarke, Paul O. Danis, Jolene K. Diedrich, Robert A. D'Ippolito, Mathieu Dupre, Natalia Gasilova, Ying Ge, Young Ah Goo, David R. Goodlett, Sylvester Greer, Kim F. Haselmann, Lidong He, Christopher L. Hendrickson, Joshua D. Hinkle, Matthew Holt, Sam Hughes, Donald F. Hunt, Neil L. Kelleher, Anton N. Kozhinov, Ziqing Lin, Christian Malosse, Alan G. Marshall, Laure Menin, Robert J. Millikin, Konstantin O. Nagornov, Simone Nicolardi, Ljiljana Pasa-Tolic, Stuart Pengelley, Neil R. Quebbemann, Anja Resemann, Wendy Sandoval, Richa Sarin, Nicholas D. Schmitt, Jeffrey Shabanowitz, Jared B. Shaw, Michael R. Shortreed, Lloyd M. Smith, Frank Sobott, Detlev Suckau, Timothy Toby, Chad R. Weisbrod, Norelle C. Wildburger, John R. Yates, Sung Hwan Yoon, Nicolas L. Young, Mowei Zhou
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Limnology
Jeffrey A. Hawkes, Juliana D'Andrilli, Jeffrey N. Agar, Mark P. Barrow, Stephanie M. Berg, Nuria Catalan, Hongmei Chen, Rosalie K. Chu, Richard B. Cole, Thorsten Dittmar, Remy Gavard, Gerd Gleixner, Patrick G. Hatcher, Chen He, Nancy J. Hess, Ryan H. S. Hutchins, Amna Ijaz, Hugh E. Jones, William Kew, Maryam Khaksari, Diana Catalina Palacio Lozano, Jitao Lv, Lynn R. Mazzoleni, Beatriz E. Noriega-Ortega, Helena Osterholz, Nikola Radoman, Christina K. Remucal, Nicholas D. Schmitt, Simeon K. Schum, Quan Shi, Carsten Simon, Gabriel Singer, Rachel L. Sleighter, Aron Stubbins, Mary J. Thomas, Nikola Tolic, Shuzhen Zhang, Phoebe Zito, David C. Podgorski
LIMNOLOGY AND OCEANOGRAPHY-METHODS
(2020)
Article
Biochemistry & Molecular Biology
Amanda R. Clark, Elizabeth C. Randall, Begona G. C. Lopez, Michael S. Regan, Jeffrey N. Agar, Benjamin J. Andreone, Chenghua Gu, Nathalie Y. R. Agar
Summary: Omega-3 phospholipid species in brain endothelial cells play a crucial role in maintaining low transcytosis rate and regulating the blood brain barrier mechanism. Advanced mass spectrometry imaging techniques were used to map the spatial distribution of these phospholipids in the brain, and the impact of omega-3 dietary deprivation was explored on the brain phospholipid profile. The study identified unique spatial distribution of DHA-containing phospholipids and changes in phospholipid species under omega-3 deficiency.
ACS CHEMICAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Krishna C. Aluri, Md Amin Hossain, Ninad Kanetkar, Brandon C. Miller, Matthew G. Dowgiallo, Durgalakshmi Sivasankar, Matthew R. Sullivan, Roman Manetsch, Tania Konry, Adam Ekenseair, Jeffrey N. Agar
Summary: This study presents a novel class of cross-linkers, cyclic thiosulfinates, for the facile synthesis of biodegradable hydrogels. The synthesized hydrogel can release proteins in vitro and support cell growth with acceptable cytotoxicity. The hydrogel can be modulated in mechanical properties and degradation kinetics with physiological concentrations of glutathione.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Morgan R. Packer, Jillian A. Parker, Jean K. Chung, Zhenlu Li, Young Kwang Lee, Trinity Cookis, Hugo Guterres, Steven Alvarez, Md Amin Hossain, Daniel P. Donnelly, Jeffrey N. Agar, Lee Makowski, Matthias Buck, Jay T. Groves, Carla Mattos
Summary: Studies demonstrate that Raf-Ras binding domain (Raf-RBD) can induce Ras dimerization at low surface densities and in solution, with robust connections between two Raf-RBD D113 residues confirmed by molecular dynamics simulations. These results suggest that Raf-RBD binding and Ras dimerization occur together, forming a high-affinity signaling complex.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Begona G. C. Lopez, Ishwar N. Kohale, Ziming Du, Ilya Korsunsky, Walid M. Abdelmoula, Yang Dai, Sylwia A. Stopka, Giorgio Gaglia, Elizabeth C. Randall, Michael S. Regan, Sankha S. Basu, Amanda R. Clark, Bianca-Maria Marin, Ann C. Mladek, Danielle M. Burgenske, Jeffrey N. Agar, Jeffrey G. Supko, Stuart A. Grossman, Louis B. Nabors, Soumya Raychaudhuri, Keith L. Ligon, Patrick Y. Wen, Brian Alexander, Eudocia Q. Lee, Sandro Santagata, Jann Sarkaria, Forest M. White, Nathalie Y. R. Agar
Summary: The study developed an integrative platform using mass spectrometry imaging, phosphoproteomics, and multiplexed tissue imaging to map drug distribution, target engagement, and adaptive response in glioblastoma. The platform identified new markers of molecular response to adavosertib and demonstrated potential in studying patient's response to the drug in clinical trials. This approach may provide valuable insights for optimizing clinical trial design and guiding future application into clinical practice.
Article
Multidisciplinary Sciences
Walid M. Abdelmoula, Begona Gimenez-Cassina Lopez, Elizabeth C. Randall, Tina Kapur, Jann N. Sarkaria, Forest M. White, Jeffrey N. Agar, William M. Wells, Nathalie Y. R. Agar
Summary: This study demonstrates the application of artificial intelligence in mining Mass Spectrometry Imaging (MSI) data to reveal biologically relevant metabolomic and proteomic information acquired from different mass spectrometry platforms. By utilizing a fully connected variational autoencoder, the researchers developed the msiPL method to learn and visualize the underlying non-linear spectral manifold in MSI data, uncovering biologically relevant clusters of tissue anatomy and tumor heterogeneity in various tissue types.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Walid M. Abdelmoula, Sylwia A. Stopka, Elizabeth C. Randall, Michael Regan, Jeffrey N. Agar, Jann N. Sarkaria, William M. Wells, Tina Kapur, Nathalie Y. R. Agar
Summary: This paper proposes a deep learning model, massNet, for the analysis of mass spectrometry imaging (MSI) data. The massNet model achieves better accuracy and speed compared to traditional machine learning methods.
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Biochemistry & Molecular Biology
Anya B. Zhong, Isabella H. Muti, Stephen J. Eyles, Richard W. Vachet, Kristen N. Sikora, Cedric E. Bobst, David Calligaris, Sylwia A. Stopka, Jeffery N. Agar, Chin-Lee Wu, Mari A. Mino-Kenudson, Nathalie Y. R. Agar, David C. Christiani, Igor A. Kaltashov, Leo L. Cheng
Summary: This article presents the application of a multiplatform approach combining NMR and MS imaging in metabolomics studies of human prostate and lung cancers. The combined analysis enhances the ability to conduct comprehensive metabolomics research.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)