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
Cell Biology
Huriye Ercan, Ulrike Resch, Felicia Hsu, Goran Mitulovic, Andrea Bileck, Christopher Gerner, Jae-Won Yang, Margarethe Geiger, Ingrid Miller, Maria Zellner
Summary: Proteomics is an essential analytical technique for studying biological systems using different proteins. The study compared the qualitative and quantitative performance of two commonly used proteomics techniques, label-free shotgun and 2D-DIGE, using six technical and three biological replicates of the human prostate carcinoma cell line DU145. The results showed that label-free shotgun quickly provides an annotated proteome but with reduced robustness compared to 2D-DIGE, which offers qualitative and quantitative information on proteoforms and post-translational modifications. However, the 2D-DIGE technique requires more time and manual work. Ultimately, this work highlights the different outputs and applications of these two techniques for biological research.
Article
Chemistry, Analytical
Kevin Jeanne Dit Fouque, Samuel A. Miller, Khoa Pham, Natarajan Bhanu, Yarixa L. Cintron-Diaz, Dennys Leyva, Desmond Kaplan, Valery G. Voinov, Mark E. Ridgeway, Melvin A. Park, Benjamin A. Garcia, Francisco Fernandez-Lima
Summary: This study demonstrates a novel analytical method for characterizing intact histone H4 proteoforms in HeLa cells and identifies multiple types and positions of modifications. The method enables fast data acquisition and high resolution, showing great potential for global proteoform analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Jeffrey Molendijk, Rui Yip, Benjamin L. Parker
Summary: We have developed a database for underrepresented post-translational modifications (PTMs) to accelerate the discovery of enriched protein modifications in experimental data. The database provides curated lists of proteins reported to be substrates of underrepresented modifications. We demonstrated the utility of the database through the analysis of previously published data. Additionally, we developed an online tool that integrates upstream transcription factor enrichment analysis with downstream pathway analysis through an easy-to-use interactive interface.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Evan A. Martin, James M. Fulcher, Mowei Zhou, Matthew E. Monroe, Vladislav A. Petyuk
Summary: Top-down proteomics is a developing field that analyzes proteins in their intact form without proteolysis. However, limitations in instrumentation and data interpretation have hindered its progress. TopPICR is a companion R package that extends the capabilities of the popular proteoform identification tool, TopPIC, to label-free proteoform quantification. The pipeline includes several key steps, such as filtering identifications and compiling feature intensities, and the output is compatible with downstream data analysis packages from the Bioconductor project.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Diogo B. Lima, Mathieu Dupre, Magalie Duchateau, Quentin Giai Gianetto, Martial Rey, Mariette Matondo, Julia Chamot-Rooke
Summary: The software can integrate data from multiple experiments and search engines, enabling rapid and easy visualization, validation, and comparison of proteoform sequences with high performance. The effectiveness of the method was demonstrated on a large-scale Escherichia coli dataset, where ProteoCombiner accurately shortlisted proteoforms identified by multiple search engines.
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.
Review
Biochemistry & Molecular Biology
Irene Messana, Barbara Manconi, Tiziana Cabras, Mozhgan Boroumand, Maria Teresa Sanna, Federica Iavarone, Alessandra Olianas, Claudia Desiderio, Diana Valeria Rossetti, Federica Vincenzoni, Cristina Contini, Giulia Guadalupi, Antonella Fiorita, Gavino Faa, Massimo Castagnola
Summary: In this review, the main post-translational modifications leading to multiple proteoforms in the human salivary proteome are extensively described, along with their potential role. The majority of the data reported in this review were obtained through over twenty-five years of research on human saliva, primarily using a top-down strategy. Various proteolytic cleavage products, salivary protein families, phospho-proteome, sulfo-proteomes, glycation, enzymatic glycosylation, citrullination, N- and C-terminal post-translational modifications, and miscellaneous other modifications are discussed in different sections of the manuscript. Furthermore, the impact and relevance of these findings in the development of new diagnostic biomarkers for clinical practice are emphasized.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Konrad Winkels, Tomas Koudelka, Philipp T. Kaulich, Matthias Leippe, Andreas Tholey
Summary: Top-down proteomics (TDP) can provide additional information about post-translational modifications and C-termini. In this study, TDP workflows were used to analyze the proteome of Caenorhabditis elegans, and the identified proteoforms were validated using a bottom-up proteomics (BUP) approach. The results showed low overlap between the two methods, with caveats in both workflows contributing to this. The study also demonstrated the applicability of reductive dimethylation in TDP to confirm biological N-termini.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Analytical
Taran Driver, Vitali Averbukh, Leszek J. Frasinski, Jon P. Marangos, Marina Edelson-Averbukh
Summary: Two-dimensional partial covariance mass spectrometry (2D-PC-MS) utilizes fragment ion abundance fluctuations in tandem mass spectra to accurately identify intact protein ions, showing higher specificity and resolution compared to one-dimensional (1D) tandem mass spectrometry (MS/MS).
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Emily A. Chapman, Timothy J. Aballo, Jake A. Melby, Tianhua Zhou, Scott J. Price, Kalina J. Rossler, Ienglam Lei, Paul C. Tang, Ying Ge
Summary: This study investigated the changes in sarcomeric proteins in the myocardia of ischemic cardiomyopathy (ICM) patients using liquid chromatography-mass spectrometry (LC-MS). The results revealed altered phosphorylation and expression of several sarcomeric proteins in ICM hearts, indicating severe dysregulation of the contractile apparatus.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Yutong Jin, Yunyu Yi, Bernice Yeung
Summary: Deamidation of asparagine and glutamine alters protein structures and affects chemical and biological properties, and is associated with aging and diseases. Mass spectrometry has been employed to identify deamidated protein species and sites for comprehensive characterization, with top-down and middle-down MS methods providing new strategies for deamidation analysis.
Article
Biochemical Research Methods
Andrea M. Brunner, Philip Lossl, Paul P. Geurink, Huib Ovaa, P. Albanese, A. F. Maarten Altelaar, Albert J. R. Heck, Richard A. Scheltema
Summary: Top-down proteomics combined with bioinformatics approaches can improve the localization and quantification of protein modifications, even for positional isomers with the same number of modifications at different sites. This method shows promising results in characterizing multiple modified proteins and estimating the stoichiometry of phosphorylated sites.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Biochemical Research Methods
Jonathan Dhenin, Diogo Borges Lima, Mathieu Dupre, Julia Chamot-Rooke
Summary: This new software tool allows easy visualization of fragment ions and rapid evaluation of key experimental parameters for the analysis of intact proteins. It can process data obtained from different software and is useful for top-down proteomics.
Article
Chemistry, Analytical
Philipp T. Kaulich, Liam Cassidy, Konrad Winkels, Andreas Tholey
Summary: In top-down proteomics, pre-fractionation is crucial for high confidence identification of proteoforms and increased proteome coverage. The use of field asymmetric ion mobility spectrometry (FAIMS) has shown to be beneficial, but only external compensation voltage (CV) stepping has been demonstrated. This study investigated the use of internal CV stepping for single-shot TD analysis and optimized MS parameters for different CVs. The optimized multi-CV method significantly increased the number of identified protein groups and proteoforms without increasing measurement time.
ANALYTICAL CHEMISTRY
(2022)
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
Chemistry, Analytical
Gregory W. Vandergrift, William Kew, Jessica K. Lukowski, Arunima Bhattacharjee, Andrey Liyu, Elizabeth A. Shank, Ljiljana Pasa-Tolic, Venkateshkumar Prabhakaran, Christopher R. Anderton
Summary: This study combines nanospray desorption electrospray ionization mass spectrometry with 21T FTICR MS, enabling high-resolution and accurate ambient sampling and imaging. By conducting experiments on biological samples and imaging rat brain tissue, isotopic fine structure (IFS) information can be obtained, providing further confidence in molecular annotation.
ANALYTICAL CHEMISTRY
(2022)
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.
Article
Multidisciplinary Sciences
Sung-Hwan Cho, Katalin Toth, Daewon Kim, Phuc H Vo, Chung-Ho Lin, Pubudu P. Handakumbura, Albert Rivas Ubach, Sterling Evans, Ljiljana Pasa-Tolic, Gary Stacey
Summary: The mevalonate pathway is crucial for cellular processes in both animals and plants. In plants, it affects growth, development, and response to stress. The interaction between mevalonate kinase and extracellular ATP receptor P2K1, with phosphorylation impacting plant metabolism, emphasizes the significance of purinergic signaling and the role of eATP in influencing plant metabolic pathways.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Jesse W. Wilson, Aivett Bilbao, Juan Wang, Yen-Chen Liao, Dusan Velickovic, Roza Wojcik, Marta Passamonti, Rui Zhao, Andrea F. G. Gargano, Vincent R. Gerbasi, Ljiljana Pasa-Tolicprime, Scott E. Baker, Mowei Zhou
Summary: SARS-CoV-2 cellular infection is mediated by heavily glycosylated spike protein. Recombinant spike protein and receptor-binding domain (RBD) play important roles in seropositivity assays and potential vaccines against viral infection. Liquid chromatography coupled to mass spectrometry is used to characterize post-translational modifications, including glycosylation. The HILIC top-down MS platform shows great potential in resolving heterogeneous glycoproteins for quality control applications.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Xuan Wang, Zhongcheng Shi, Hsin-Yi Lu, Jean J. Kim, Wen Bu, Jose A. Villalobos, Dimuthu N. Perera, Sung Yun Jung, Tao Wang, Sandra L. Grimm, Bethany C. Taylor, Kimal Rajapakshe, Hyekyung Park, Julia Wulfkuhle, Nicolas L. Young, Yi Li, Cristian Coarfa, Dean P. Edwards, Shixia Huang
Summary: This study established an antibody-based reverse phase protein array platform for comprehensive profiling of post-translational modifications of histones and histone modifier proteins. The high throughput platform provides a valuable tool for analyzing epigenetics in biological and disease studies, and has potential applications in diagnostics and therapy development.
JOURNAL OF PROTEOMICS
(2022)
Review
Microbiology
Noah W. Sokol, Eric Slessarev, Gianna L. Marschmann, Alexa Nicolas, Steven J. Blazewicz, Eoin L. Brodie, Mary K. Firestone, Megan M. Foley, Rachel Hestrin, Bruce A. Hungate, Benjamin J. Koch, Bram W. Stone, Matthew B. Sullivan, Olivier Zablocki, Jennifer Pett-Ridge
Summary: Soil microorganisms play a critical role in global biogeochemical cycles, and their metabolic functions are influenced by ecological interactions and the surrounding environment. Understanding microbial life and death can help predict soil biogeochemical dynamics.
NATURE REVIEWS MICROBIOLOGY
(2022)
Review
Cell Biology
Faith M. Joseph, Nicolas L. Young
Summary: Post-translational modifications (PTMs) of histones play a key role in DNA-based processes and contribute to cell differentiation and gene function by adding an extra layer of regulation. Variations in histone sequences within each family of histones expand the chromatin repertoire and provide further mechanisms for regulation and signaling. However, much remains unknown about variant-specific PTMs and their role in regulating chromatin due to limited technologies and appropriate reagents.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jongmin Woo, Geremy C. Clair, Sarah M. Williams, Song Feng, Chia-Feng Tsai, Ronald J. Moore, William B. Chrisler, Richard D. Smith, Ryan T. Kelly, Ljiljana Pasa-Tolic, Charles Ansong, Ying Zhu
Summary: Single-cell proteomics (scProteomics) is a powerful tool for studying cell functions in complex biological systems. However, current methods face challenges in identifying and quantifying low-abundance proteins accurately. In this study, we present a method called transferring identification based on FAIMS filtering (TIFF), which combines ion mobility-enhanced mass spectrometry acquisition and peptide identification to improve the sensitivity and accuracy of label-free scProteomics. By filtering out singly charged ions, the TIFF method extends the ion accumulation times for peptide ions. Peptide identities are determined using a three-dimensional MS1 feature matching approach. Using TIFF, we achieved unbiased proteome analysis of over 1,700 proteins in single HeLa cells, with more than 1,100 proteins consistently identified. We also applied the TIFF method to study time-dependent proteome changes in single murine macrophage cells during lipopolysaccharide stimulation.
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)
Article
Chemistry, Analytical
Kevin J. Zemaitis, Dusan Velickovic, William Kew, Kyle L. Fort, Maria Reinhardt-Szyba, Annapurna Pamreddy, Yanli Ding, Dharam Kaushik, Kumar Sharma, Alexander A. Makarov, Mowei Zhou, Ljiljana Pasa-Tolic
Summary: This study demonstrates the use of MALDI-MS imaging for direct measurement of core histone proteoforms from tissues, showing their distribution at near-cellular spatial resolution on sections of human kidney. It provides a new tool for high-throughput accurate identification of proteoforms and mapping biomolecule distributions throughout tissue sections in extended mass ranges.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Kevin J. Zemaitis, Mowei Zhou, Willia M. Kew, Ljiljana Pasa-Tolic
Summary: MALDI imaging enables the profiling of proteoforms at a near-cellular level, but identifying unknowns using only intact mass information remains a challenge. Supplementary methods, such as bottom-up and/or top-down proteomics, have been used to create experimental databases for accurate mass matching. This study demonstrates the feasibility of top-down analyses of isolated MALDI protein ions using 193 nm ultraviolet photodissociation, allowing for more comprehensive characterization of proteoforms in MALDI imaging applications.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Sara Forcisi, Franco Moritz, Christopher J. Thompson, Basem Kanawati, Jenny Uhl, Carlos Afonso, Chantal D. Bader, Aiko Barsch, Berin A. Boughton, Rosalie K. Chu, Justine Ferey, Francisco Fernandez-Lima, Celine Gueguen, Dimitri Heintz, Mario Gomez-Hernandez, Kyoung-Soon Jang, Nikolas Kessler, Vaughn Mangal, Rolf Mueller, Ryo Nakabayashi, Edith Nicol, Simone Nicolardi, Magnus Palmblad, Ljiljana Pasa-Tolic, Jacob Porter, Isabelle Schmitz-Afonso, Jong Bok Seo, Eduardo Sommella, Yuri E. M. van der Burgt, Claire Villette, Matthias Witt, Ashley Wittrig, Jeremy J. Wolff, Michael L. Easterling, Frank H. Laukien, Philippe Schmitt-Kopplin
Summary: Ultrahigh resolution mass spectrometry combined with direct infusion ionization is a fast and accurate method for untargeted metabolomics analysis. Fourier transform ion cyclotron resonance mass spectrometers play an important role in studying complex chemical systems by enabling unambiguous molecular formula assignment. Through a comparison study involving 17 laboratories worldwide, we found that five laboratories showed comparable and representative performances, providing a reference for future ring trials on blood plasma.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
Bethany C. Taylor, Nicolas L. Young
Summary: Histone proteins play a vital role in the regulation of the eukaryotic genome. This study demonstrates the first quantitative in vivo top-down analysis of histone H4 and compares the forebrains and hindbrains of differently aged mice. The results reveal differences in histone H4 post-translational modifications (PTMs) and proteoforms between brain regions and during adolescence. Lysine 20 methylation, however, remains constant with age and brain region.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Meeting Abstract
Biotechnology & Applied Microbiology
Swapna Kollu, Anusha Sairavi, Stephanie Thibert, Mowei Zhou, Xiao-Xin Sun, Mushui Dai, Ljiljana Pasa-Tolic, Hiroyuki Nakai
