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, Analytical
Ali H. Abikhodr, Vasyl Yatsyna, Ahmed Ben Faleh, Stephan Warnke, Thomas R. Rizzo
Summary: The study demonstrates a new approach using infrared spectroscopy for identifying isomers in a glycan mixture, providing a solution for identifying isomeric components in a mixture when they cannot be separated by high-resolution ion mobility spectrometry.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Francis Berthias, Dale A. Cooper-Shepherd, Frederik H. V. Holck, James I. Langridge, Ole N. Jensen
Summary: The combination of cyclic ion mobility spectrometry (cIM) and electron capture dissociation (ECD) allows for the complete separation and sequencing of large isomeric peptides, providing a new method for identifying biologically important proteoforms in complex mixtures.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
James N. Dodds, Lingjue Wang, Gary J. Patti, Erin S. Baker
Summary: The combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS) is commonly used for feature annotation in untargeted omics experiments. However, ensuring that these features originate from endogenous metabolism remains challenging. In this paper, the authors evaluate the analytical utility of incorporating ion mobility spectrometry (IMS) into LC-MS/MS isotopologue workflows and demonstrate the enhanced separation space and increased annotation confidence provided by IMS.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Holden T. Rogers, David S. Roberts, Eli J. Larson, Jake A. Melby, Kalina J. Rossler, Austin V. Carr, Kyle A. Brown, Ying Ge
Summary: We have developed a rapid and robust top-down proteomics method to extract and comprehensively characterize endogenous PLN from cardiac tissue, enabling a better understanding of its role in cardiac contractility.
ANALYTICAL CHEMISTRY
(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
Chemistry, Analytical
Francis Berthias, Matthew A. Baird, Alexandre A. Shvartsburg
Summary: Since the 1980s, D-amino acid-containing peptides (DAACPs) have been discovered in animals, showing tremendous functional specificity at extremely low levels. The introduction of the new technique differential IMS (FAIMS) has successfully separated all 18 pairs of epimer species, showcasing a 2.5X resolution increase compared to trapped IMS.
ANALYTICAL CHEMISTRY
(2021)
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
Chemistry, Analytical
Patrick O. Helmer, Ilona D. Nordhorn, Ansgar Korf, Arne Behrens, Rebecca Buchholz, Florian Zubeil, Uwe Karst, Heiko Hayen
Summary: The study focuses on identifying complex lipid species using high-resolution mass spectrometry and separation methods, with enhanced accuracy through collision cross section and TIMS technology. The main emphasis is on distinguishing isomeric and isobaric lipid classes.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Darya Hadavi, Marina Borzova, Tiffany Porta Siegel, Maarten Honing
Summary: This study aimed to develop tandem mass spectrometry-ion mobility spectrometry (MS/MS-IMS) methodologies to explore and understand the behavior of isomeric steroids in the gas-phase and rapidly separate them. Results showed that the behavior of isomeric steroids was influenced by factors such as adduct positioning and bending of the steroid ring. Data evaluation revealed the tendency of isomers to form homo-clusters in mixture solutions and assist in separation.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biochemical Research Methods
Chih-Hsiang Chang, Darien Yeung, Victor Spicer, Kosuke Ogata, Oleg Krokhin, Yasushi Ishihama
Summary: The study investigates the impact of peptide amino acid sequence on collision cross section values (CCS); ion mobility is mainly affected by the peptide's ability to solvate positively charged sites; the positioning of amino acid residues, as well as helical propensity and hydrophobicity, play important roles in the formation of extended structures.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Rebecca Brendel, Sascha Rohn, Philipp Weller
Summary: The study aimed to enhance the selectivity of IMS for isomeric monoterpenes by adding NO as a dopant, leading to the formation of additional product ions and improved discrimination of monoterpenes in volatile profiles. The use of NO as a dopant facilitated the identification of monomeric, dimeric, and trimeric ion clusters, shedding light on isomerization mechanisms in the ion signals.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Jonathan Dhenin, Valerie Lafont, Mathieu Dupre, Alain Krick, Christine Mauriac, Julia Chamot-Rooke
Summary: Monoclonal antibodies (mAbs) are widely used in biopharmaceutical therapeutics, and assessing their in vivo stability is crucial for drug development. Current analytical techniques for pharmacokinetics (PK) studies, such as ligand-binding assay (LBA) and liquid chromatography-mass spectrometry (LC-MS), analyze mAbs at the peptide level, which limits the characterization of different mAb proteoforms. In this study, we propose a workflow using automated immunocapture followed by top-down and middle-down LC-MS/MS approaches to characterize mAb proteoforms in mouse plasma. The workflow was demonstrated using pembrolizumab as a model and the performance of two Orbitrap platforms was compared.
Article
Chemistry, Multidisciplinary
David S. Roberts, Morgan Mann, Brad H. Li, Donguk Kim, Allan R. Braiser, Song Jin, Ying Ge
Summary: The SARS-CoV-2 Omicron variant has multiple spike mutations that enhance transmissibility and evasion of neutralizing antibodies. By using high-resolution mass spectrometry, researchers have identified novel glycosite and glycoform changes in the Omicron variant, which can provide insights for the rational design of vaccines and therapeutics.
Article
Chemistry, Multidisciplinary
David S. Roberts, Morgan Mann, Jake A. Melby, Eli J. Larson, Yanlong Zhu, Allan R. Brasier, Song Jin, Ying Ge
Summary: Researchers have successfully elucidated the complete structure of newly discovered O-glycans on the S protein regional-binding domain (SR-BD) of the SARS-CoV-2 virus through a hybrid mass spectrometry approach. This method can provide insights into the interactions between the virus and host cells, laying a foundation for understanding the functional roles of O-glycans in SARS-CoV-2 and other glycoproteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Immunology
Barbara B. Esteves, Marcella N. Melo-Braga, Vladimir Gorshkov, Thiago Verano-Braga, Martin R. Larsen, Celia M. F. Gontijo, Patricia F. Quaresma, Helida M. Andrade
Summary: In this study, differential protein expression in Leishmania braziliensis strains causing atypical cutaneous lesions compared to strains causing typical lesions was identified. The atypical strains showed upregulation of proteins related to macrophage survival, antimony resistance, and peroxidase activity. Additionally, potential drug and vaccine targets were identified. These findings contribute to the understanding of atypical cutaneous leishmaniasis and provide new insights for treatment and prevention strategies.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Filipe Alex da Silva, Lucas Rodrigues-Ribeiro, Marcella Nunes Melo-Braga, Danielle Gomes Passos-Silva, Walkyria Oliveira Sampaio, Vladimir Gorshkov, Frank Kjeldsen, Thiago Verano-Braga, Robson Augusto Souza Santos
Summary: This study investigates the signaling pathways of alamandine in both tumor and non-tumor cells, revealing its antiproliferative effect by activating the transcription factor FoxO1, negatively regulating the PI3K/AKT/mTOR pathway, and inducing metabolic shift in tumor cells.
Article
Immunology
Daria V. Evsyutina, Tatiana A. Semashko, Maria A. Galyamina, Sergey I. Kovalchuk, Rustam H. Ziganshin, Valentina G. Ladygina, Gleb Y. Fisunov, Olga V. Pobeguts
Summary: This study compared the proteome of Mycoplasma hominis cultivated on two different energy sources and found significant differences in growth rate, antibiotic sensitivity, and biofilm formation. The energy source strongly influenced the synthesis of enzymes related to RNA modifications, ribosome assembly, and membrane-associated proteins. The findings provide insights into the energy source-dependent control of pathogenicity factors and the interaction between growth rate and fitness in genome-reduced bacteria.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Daria Evsyutina, Gleb Y. Fisunov, Olga Pobeguts, Sergey Kovalchuk, Vadim M. Govorun
Summary: This study developed a CRISPRi system for gene repression in mycoplasmas, which showed minimal impact on mycoplasma growth. The functionality of the system was confirmed by targeting key genes and observing their decreased expression levels. This system can be a powerful tool for discovering gene functions, deciphering regulatory networks, and identifying novel drug targets for controlling mycoplasma infections.
Article
Biochemistry & Molecular Biology
Marta Ignasiak-Kciuk, Karolina Nowicka-Bauer, Marta Grzechowiak, Tina Ravnsborg, Kamil Frackowiak, Ole N. Jensen, Mariusz Jaskolski, Bronislaw Marciniak
Summary: This study investigates the sensitized photo-oxidation reaction using carboxybenzophenone (CB) as a sensitizer and a PR-10 protein (MtN13) as a quencher. It reveals the specific binding of CB in the protein's hydrophobic cavity and the amino acid residues creating adducts with the sensitizer. The study also elucidates the mechanisms of CB quenching and the influence of neighboring groups on the oxidation process.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Kseniia A. Palkina, Anastasia V. Balakireva, Olga A. Belozerova, Tatiana V. Chepurnykh, Nadezhda M. Markina, Sergey I. Kovalchuk, Aleksandra S. Tsarkova, Alexander S. Mishin, Ilia V. Yampolsky, Karen S. Sarkisyan
Summary: Hispidin is a polyketide found in plants and fungi, which functions as a precursor of luciferin in bioluminescent fungi. The absence of two domains with predicted ketoreductase and dehydratase activities in hispidin synthases distinguishes them from non-bioluminescent fungi. Our investigation suggests that the loss of these domains in evolution led to the emergence of bioluminescence and the production of hispidin.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Biochemical Research Methods
Michael R. Hoopmann, Veit Schwaemmle, Magnus Palmblad
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Mette Louise Trempenau, Mikkel Bruhn Schuster, Sachin Pundhir, Mafalda Araujo Pereira, Adrija Kalvisa, Marta Tapia, Jinyu Su, Ying Ge, Bauke de Boer, Alexander Balhuizen, Frederik Otzen Bagger, Pavel Shliaha, Patrycja Sroczynska, Julian Walfridsson, Kirsten Gronbaek, Kim Theilgaard-Moench, Ole N. N. Jensen, Kristian Helin, Bo T. T. Porse
Summary: This study identifies the Histone 3 Lysine 4 (H3K4) demethylase KDM5C as a tumor suppressor in acute myeloid leukemia (AML). Decreased KDM5C expression leads to increased cell growth in AML cell lines and mouse models. Mechanistically, KDM5C acts as a transcriptional repressor through its demethylase activity, resulting in upregulation of immature genes marked by H3K4me3. The association of KDM5C levels with long-term disease-free survival in female AML patients highlights the clinical relevance of this finding.
Meeting Abstract
Biochemistry & Molecular Biology
Karolina Nowicka-Bauer, Marta Ignasiak-Kciuk, Marta Grzechowiak, Tina Ravensborg, Kamil Frackowiak, Ole N. Jensen, Mariusz Jaskolski, Bronislaw Marciniak
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Francis Berthias, Dale A. Cooper-Shepherd, Frederik H. V. Holck, James I. Langridge, Ole N. Jensen
Summary: The combination of cyclic ion mobility spectrometry (cIM) and electron capture dissociation (ECD) allows for the complete separation and sequencing of large isomeric peptides, providing a new method for identifying biologically important proteoforms in complex mixtures.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Tomiris T. Kusainova, Daria D. Emekeeva, Elizaveta M. Kazakova, Vladimir A. Gorshkov, Frank Kjeldsen, Mikhail L. Kuskov, Alexey N. Zhigach, Irina P. Olkhovskaya, Olga A. Bogoslovskaya, Natalia N. Glushchenko, Irina A. Tarasova
Summary: In recent years, ultrafast liquid chromatography/mass spectrometry methods have been extensively developed for proteome profiling in biochemical studies. This study aimed to adapt these methods for quantitative profiling of molecular changes in wheat seedlings in response to seed treatment with iron compounds.
BIOCHEMISTRY-MOSCOW
(2023)
Article
Medicine, Research & Experimental
Vignesh Ramesh, Paradesi Naidu Gollavilli, Luisa Pinna, Mohammad Aarif Siddiqui, Adriana Martinez Turtos, Francesca Napoli, Yasmin Antonelli, Aldo Leal-Egana, Jesper Foged Havelund, Simon Toftholm Jakobsen, Elisa Le Boiteux, Marco Volante, Nils Joakim Faergeman, Ole N. Jensen, Rasmus Siersbaek, Kumar Somyajit, Paolo Ceppi
Summary: This study found an inverse association between short-chain fatty acids and EMT in non-small cell lung cancer patients. In vitro experiments showed that propionate treatment enhanced the epithelial transcriptional program and reduced the EMT phenotype in lung cancer cell lines. Animal experiments also confirmed that propionate can reduce lung cancer metastasis and lymph node spread. Further mechanistic investigation revealed that propionate treatment caused chromatin remodeling through p300-mediated histone acetylation.
EMBO MOLECULAR MEDICINE
(2023)
Article
Biochemical Research Methods
Pelayo A. A. Penanes, Vladimir Gorshkov, Mark V. V. Ivanov, Mikhail V. V. Gorshkov, Frank Kjeldsen
Summary: Current proteomics approaches often neglect the negative ionization mode, leading to inefficient identification of acidic peptides. This study introduces the DirectMS1 method, which achieves the highest protein identification rate in the negative ionization mode. By optimizing separation and experimental conditions, over 1000 proteins were identified in a human cell line, comparable to MS/MS-based analyses. The study also highlights the potential of using the same digestion procedures in both positive and negative ion modes.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Cell Biology
Vincent Gaggioli, Calvin S. Y. Lo, Nazaret Reveron-Gomez, Zuzana Jasencakova, Heura Domenech, Hong Nguyen, Simone Sidoli, Andrey Tvardovskiy, Sidrit Uruci, Johan A. Slotman, Yi Chai, Joao G. S. C. Souto Goncalves, Eleni Maria Manolika, Ole N. Jensen, David Wheeler, Sriram Sridharan, Sanjiban Chakrabarty, Jeroen Demmers, Roland Kanaar, Anja Groth, Nitika Taneja
Summary: Chromatin signalling cascade, regulated by a checkpoint, activates the histone methyltransferase EHMT2/G9a to assemble heterochromatin at stressed replication forks. G9a, together with SUV39h1, induces chromatin compaction through accumulating repressive modifications, H3K9me1/me2/me3, at stressed replication forks. Untimely heterochromatin disassembly by demethylase KDM3A exposes forks to PRIMPOL-mediated genome instability, leading to chemotherapeutic drug sensitivity.
NATURE CELL BIOLOGY
(2023)