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
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
Multidisciplinary Sciences
Yu Fu, Zhenglin Zhu, Geng Meng, Rijun Zhang, Yueping Zhang
Summary: Post-translational modifications of histone proteins play a crucial role in gene expression and cell fate decisions. Developing efficient methods for introducing mutations to histones is vital for studying these modifications. By utilizing a CRISPR-Cas9 based system in yeast cells, researchers successfully generated multiple histone mutants, presenting a valuable tool for the field of epigenetics.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Analytical
Yue Sun, Yu Liang, Chao Wang, Baofeng Zhao, Zhen Liang, Xiaodan Zhang, Yukui Zhang, Lihua Zhang
Summary: Comprehensive characterization of membrane proteins at the level of proteoforms in complex biological samples by top-down mass spectrometry (MS) is of vital importance in revealing their precise functions. However, severe peak broadening in the separation of hydrophobic membrane proteins, caused by resistance to mass transfer and strong adsorption on separation materials, leads to MS spectra overlap and signal suppression, which makes against the in-depth research on membrane proteoforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Lai Shi, Karen Aymonnier, Denisa D. Wagner
Summary: PAD4 catalyzes posttranslational modification by converting protein arginine to citrulline, promoting histone H4-induced NET formation, while citrullinated histone H4 may reduce NET formation, potentially playing a role in the pathology of NETs.
Article
Biotechnology & Applied Microbiology
Narges Fatemiyan, James R. Davie
Summary: H4K20me1 is a modification that is broadly distributed along genes and is associated with expressed and repressed genes. In contrast, H3K4me3 is a modification that is localized to the 5' end of most expressed genes in vertebrate cells. This study found that H4K20me1 is associated with expressed genes in estrogen receptor-positive breast cancer MCF7 cells and erythroleukemic K562 cells. The broad H4K20me1 domain marks the gene bodies of expressed genes, but not the promoter or enhancer regions. There is little overlap between the genes marked with H4K20me1 and those marked with H3K4me3. The distribution of H4K20me1 and H3K79me2 along expressed gene bodies is similar, suggesting a relationship between the enzymes involved in these histone modifications.
Article
Chemistry, Analytical
Chao Wang, Yu Liang, Baofeng Zhao, Zhen Liang, Lihua Zhang, Yukui Zhang
Summary: This study successfully prepared ethane-bridged hybrid monoliths with well-defined large mesopores, which achieved high peak capacity and separation efficiency in top-down proteomic analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Jake A. Melby, David S. Roberts, Eli J. Larson, Kyle A. Brown, Elizabeth F. Bayne, Song Jin, Ying Ge
Summary: Top-down proteomics is a powerful technology for comprehensively characterizing proteoforms and understanding protein functions, disease mechanisms, and biomarkers. However, challenges in protein solubility, data analysis, and proteome complexity remain. Recent technological developments include the development of new surfactants, nanoparticles for enriching proteoforms, and strategies for multi-dimensional chromatography separation of proteins.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
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
Biochemistry & Molecular Biology
Yanlei Hu, Mengyue Shi, Liang Liu, Juan Yu, Yimin Fan
Summary: This study successfully prepared silk nanocrystal-based hydrogels through pretreatment and oxidation of natural silk fibers, showcasing excellent mechanical properties and highly porous, interconnected, and crisscrossed network nanostructures. This has significant implications for tissue regeneration and the future use of porous scaffolds in bioengineering applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemical Research Methods
Allen Po, Claire Eyers
Summary: Top-down proteomics aims to identify and analyze intact proteoforms extracted from biological samples. However, defining and pinpointing post-translational modifications on intact proteins remains a challenge. This is crucial for understanding the specific roles and structure-function relationships of proteins.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Materials Science, Multidisciplinary
Sailing Zhu, Subir Kumar Biswas, Zhe Qiu, Yiying Yue, Qiliang Fu, Feng Jiang, Jingquan Han
Summary: Transparent wood-based materials (TWMs) have gained significant attention due to their transparency, sustainability, and multifunctionality. TWMs produced using a top-down approach preserve the natural hierarchical structure of wood and offer high production efficiency and scalability. Various techniques, such as wood nanotechnologies and polymer impregnation, have been developed to fabricate TWMs with similar sustainability and optical transmittance. This review provides a comprehensive summary of the state-of-the-art for transparent wood and transparent wood films, highlighting the relationship between process, structure, property, and application perspectives in TWM science.
PROGRESS IN MATERIALS SCIENCE
(2023)
Article
Biochemical Research Methods
Qianyi Wang, Fei Fang, Qianjie Wang, Liangliang Sun
Summary: The characterization of histone proteoforms with various post-translational modifications is crucial for understanding their role in epigenetic control of gene expression. This study presents a novel approach combining capillary zone electrophoresis, ion mobility spectrometry, and mass spectrometry for online multi-dimensional separations of histone proteoforms. The results demonstrate that this technique can greatly improve the identification of histone proteoforms and provide a high sensitivity tool for their comprehensive characterization.
Article
Biochemical Research Methods
Richard D. LeDuc, Veit Schwammle, Michael R. Shortreed, Anthony J. Cesnik, Stefan K. Solntsev, Jared B. Shaw, Maria J. Martin, Juan A. Vizcaino, Emanuele Alpi, Paul Danis, Neil L. Kelleher, Lloyd M. Smith, Ying Ge, Jeffrey N. Agar, Julia Chamot-Rooke, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin
JOURNAL OF PROTEOME RESEARCH
(2018)
Article
Multidisciplinary Sciences
Ioanna Ntai, Luca Fornelli, Caroline J. DeHart, Josiah E. Hutton, Peter F. Doubleday, Richard D. LeDuc, Alexandra J. van Nispen, Ryan T. Fellers, Gordon Whiteley, Emily S. Boja, Henry Rodriguez, Neil L. Kelleher
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Biochemical Research Methods
Richard D. LeDuc, Ryan T. Fellers, Bryan P. Early, Joseph B. Greer, Daniel P. Shams, Paul M. Thomas, Neil L. Kelleher
MOLECULAR & CELLULAR PROTEOMICS
(2019)
Review
Biochemical Research Methods
Leah Schaffer, Robert J. Millikin, Rachel M. Miller, Lissa C. Anderson, Ryan T. Fellers, Ying Ge, Neil L. Kelleher, Richard D. LeDuc, Xiaowen Liu, Samuel H. Payne, Liangliang Sun, Paul M. Thomas, Trisha Tucholski, Zhe Wang, Si Wu, Zhijie Wu, Dahang Yu, Michael R. Shortreed, Lloyd M. Smith
Article
Biochemistry & Molecular Biology
Xiaoxiao Huang, Richard D. LeDuc, Luca Fornelli, Alissa J. Schunter, Richard L. Bennett, Neil L. Kelleher, Jonathan D. Licht
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Letter
Biochemical Research Methods
Lloyd M. Smith, Paul M. Thomas, Michael R. Shortreed, Leah V. Schaffer, Ryan T. Fellers, Richard D. Leduc, Trisha Tucholski, Ying Ge, Jeffrey N. Agar, Lissa C. Anderson, Julia Chamot-Rooke, Joseph Gault, Joseph A. Loo, Ljiljana Pasa-Tolic, Carol V. Robinson, Hartmut Schlueter, Yury O. Tsybin, Marta Vilaseca, Juan Antonio Vizcaino, Paul O. Danis, Neil L. Kelleher
Article
Biochemical Research Methods
Hae-Min Park, Rosalba Satta, Roderick G. Davis, Young Ah Goo, Richard D. LeDuc, Ryan T. Fellers, Joseph B. Greer, Elena Romanova, Stanislav S. Rubakhin, Rex Tai, Paul M. Thomas, Jonathan Sweedler, Neil L. Kelleher, Steven M. Patrie, Amy W. Lasek
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Amanda L. Wong, Nicholas N. Totah, Anthony T. Iavarone, James J. Pesavento
Article
Multidisciplinary Sciences
Nathaniel F. Henning, Richard D. LeDuc, Kelly A. Even, Monica M. Laronda
SCIENTIFIC REPORTS
(2019)
Article
Biochemical Research Methods
Ashley N. Ives, Taojunfeng Su, Kenneth R. Durbin, Bryan P. Early, Henrique dos Santos Seckler, Ryan T. Fellers, Richard D. LeDuc, Luis F. Schachner, Steven M. Patrie, Neil L. Kelleher
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Biochemical Research Methods
Sarah R. Rommelfanger, Mowei Zhou, Henna Shaghasi, Shin-Cheng Tzeng, Bradley S. Evans, Ljiljana Pasa-Toli, James G. Umen, James J. Pesavento
Summary: An updated analysis of linker and core histone proteins in the green microalga Chlamydomonas reinhardtii was conducted using top-down mass spectrometry, revealing 86 proteoforms. Variants with high levels of acetylation were identified among the canonical histones, emphasizing the presence of diverse protein forms in this organism.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Cardiac & Cardiovascular Systems
John T. Wilkins, Henrique S. Seckler, Jonathan Rink, Philip D. Compton, Luca Fornelli, C. Shad Thaxton, Rich LeDuc, David Jacobs, Peter F. Doubleday, Allan Sniderman, Donald M. Lloyd-Jones, Neil L. Kelleher
Summary: This study characterizes the associations between different proteoforms of ApoAI and ApoAII with cardiometabolic indices, showing that the relationships are proteoform-specific. These results demonstrate the potential for precise chemical characterization of human apolipoproteins to provide insights into the complex pathways through which proteins mediate health and disease.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2021)
Article
Biochemistry & Molecular Biology
Michael A. R. Hollas, Matthew T. Robey, Ryan T. Fellers, Richard D. LeDuc, Paul M. Thomas, Neil L. Kelleher
Summary: The Human Proteoform Atlas is an online repository storing experimentally verified human proteoforms, using a FAIR system to assign persistent identifiers and facilitate tracking and organization. Users can submit new proteoforms via email, and future iterations will help in studying and organizing these protein molecules further.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Richard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L. Kelleher, Paul M. Thomas, Juan Antonio Vizcaino
Summary: It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence. The ProForma 2.0 notation aims to unify the representation of proteoforms and peptidoforms, supporting different proteomics approaches and allowing the encoding of highly modified proteins and peptides using a human- and machine-readable string.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Ashley N. Ives, Henry A. Dunn, Hamid Samareh Afsari, Henrique Dos Santos Seckler, Max J. Foroutan, Erica Chavez, Rafael D. Melani, Ryan T. Fellers, Richard D. LeDuc, Paul M. Thomas, Kirill A. Martemyanov, Neil L. Kelleher, Reza Vafabakhsh
Summary: G protein-coupled receptors (GPCRs) are the largest family of membrane receptors in humans and play a crucial role in regulating human physiology. Different phosphorylation states can occur on a single GPCR and each state encodes a unique signaling outcome. Traditional proteomic techniques provide limited quantitative information about GPCR phosphorylation states. This study presents a middle-down proteomic strategy and parallel reaction monitoring (PRM) to quantify the phosphorylation states of the C-terminal tail of mGluR2, a type of GPCR.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)