Article
Chemistry, Analytical
Xian-Na Wang, Bin Li
Summary: Gold nanoparticles/thiol-beta-cyclodextrin-functionalized TiO2 nanowires were prepared to enhance the performance of SALDI MS and MSI, showing superior detection sensitivity and repeatability.
ANALYTICAL CHEMISTRY
(2022)
Article
Materials Science, Multidisciplinary
Jean-Arthur Amalian, Tathagata Mondal, Evgeniia Konishcheva, Gianni Cavallo, Benoit Eric Petit, Jean-Francois Lutz, Laurence Charles
Summary: Sequence-defined synthetic polymers are being used as a medium to store information at the molecular level, with low storage capacity of readable chains being a current limitation. Ordering short oligomers on surfaces to compose long messages is an attractive alternative, and desorption electrospray ionization (DESI) is shown to be suitable for bidimensional data storage.
ADVANCED MATERIALS TECHNOLOGIES
(2021)
Article
Chemistry, Analytical
Xufang Hu, Zongping Wang, Haolin Chen, An Zhao, Nianrong Sun, Chunhui Deng
Summary: An advanced metabolic analysis tool based on highly porous metal oxides derived from metal-organic frameworks (MOFs) is developed in this study. The tool successfully differentiates and stages renal cell carcinoma (RCC), as well as identifies the size of tumors. This achievement shows promising prospects for designer matrix-based analytical tools in disease diagnosis.
ANALYTICAL CHEMISTRY
(2022)
Article
Microbiology
Eva Gato, Manuel J. Arroyo, Gema Mendez, Ana Candela, Bruno Kotska Rodino-Janeiro, Javier Fernandez, Belen Rodriguez-Sanchez, Luis Mancera, Jorge Arca-Suarez, Alejandro Beceiro, German Bou, Marina Oviano
Summary: This study proposes a machine learning approach that uses the complete cell spectra for the direct prediction of carbapenemase-producing Klebsiella pneumoniae (CPK) isolates. The method achieved high accuracy and revealed the contribution of the complete proteome to the algorithm-based classification.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Ouyang Dan, Chuanzhe Wang, Chao Zhong, Juan Lin, Gang Xu, Guane Wang, Zian Lin
Summary: In this study, novel LDI-MS substrates were designed to enhance the sensitivity of mass signals and achieve high accuracy diagnosis of different saccharides and central precocious puberty (CPP).
Review
Chemistry, Analytical
Katerina V. Djambazova, Jacqueline M. Van Ardenne, Jeffrey M. Spraggins
Summary: Imaging mass spectrometry allows for the untargeted mapping of biomolecules directly from tissue sections, with widespread clinical applicability in disease diagnosis and classification. This review summarizes the two most widely employed IMS technologies and their advancements in biomedical applications.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Ying Feng, Xianhu Wei, Moutong Chen, Honghui Zhu, Jumei Zhang, Youxiong Zhang, Liang Xue, Lanyan Huang, Guoyang Chen, Qihui Gu, Shi Wu, Yu Ding, Qingping Wu
Summary: This study developed a new deep semi-quantitative fingerprinting method using pseudotargeted metabolomics and deep learning techniques, achieving a prediction accuracy of Listeria monocytogenes serotypes exceeding 99%. This technology demonstrates great potential for the rapid and accurate identification of pathogens.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Margaux Fresnais, Siwen Liang, Deniz Seven, Nevena Prodanovic, Julia Sundheimer, Walter E. Haefeli, Juergen Burhenne, Remi Longuespee
Summary: The development and validation of desorption/ionization mass spectrometric assays for drug quantification in tissue sections is crucial for their widespread application in (clinical) pharmacology. Advances in desorption electrospray ionization have demonstrated its usefulness for developing targeted quantification methods that meet validation requirements. Factors such as desorption spot morphology, analytical time, and sample surface need to be considered for successful method development. This study highlights the importance of considering desorption kinetics during DESI analyses, which can help reduce analytical time, verify solvent-based drug extraction methods, and predict feasibility of imaging assays. These findings provide valuable guidance for future development of validated DESI-profiling and imaging methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Xuetong Qu, Tao Wang, Xingyue Liu, Xinrong Jiang, Xiao Liang, Jianmin Wu
Summary: A dual-mechanism-driven strategy for high-coverage detection of serum lipids was proposed, using a novel SALDI-MS target composed of composite nanostructures. The strategy enabled simultaneous detection of multiple lipid types in a fast analysis. Furthermore, the method demonstrated high sensitivity and specificity in diagnosing hepatocellular carcinoma.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemical Research Methods
Lanaia Itala Louzeiro Maciel, Ricardo Alves Bernardo, Rafael Oliveira Martins, Almir Custodio Batista Jr, Joao Victor Ataide Oliveira, Andrea Rodrigues Chaves, Boniek Gontijo Vaz
Summary: The imaging of biological tissues using mass spectrometry imaging (MSI) techniques allows for the visualization of the distribution of various metabolites, drugs, lipids, and glycans in complex samples. MSI methods like DESI-MSI and MALDI-MSI provide high sensitivity and the ability to evaluate/visualize multiple analytes in a single sample, overcoming limitations of classical microscopy techniques. This review discusses the application of DESI-MSI and MALDI-MSI in evaluating exogenous and endogenous molecules in biological samples, providing technical insights and recent research findings.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Fengjian Chu, Gaosheng Zhao, Wangyu Li, Wei Wei, Weiwei Chen, Zihan Ma, Zhan Gao, Nazifi Sani Shuaibu, Jikui Luo, Bingwen Yu, Hongru Feng, Yuanjiang Pan, Xiaozhi Wang
Summary: A microwave plasma torch-based ion/molecular reactor (MPTIR) has been developed for rapid oxidation reactions. This device can activate oxygen in the air to achieve oxidation of thioethers, alcohols, and various environmental pollutants on a millisecond scale without the use of external oxidants or catalysts. It can also accurately predict environmental pollutants and study the mechanism of atmospheric oxidative processes.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Fengjian Chu, Gaosheng Zhao, Wangyu Li, Wei Wei, Weiwei Chen, Zihan Ma, Zhan Gao, Nazifi Sani Shuaibu, Jikui Luo, Bingwen Yu, Hongru Feng, Yuanjiang Pan, Xiaozhi Wang
Summary: A microwave plasma torch-based ion/molecular reactor (MPTIR) has been developed for creating and monitoring rapid oxidation reactions without the addition of external oxidants or catalysts. The oxidation products from the MPTIR match those of the long-term environmental oxidative process, and two unreported environmental compounds were identified in actual water samples using this device.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Yuanqing Luo, Xiaoyong Zhao, Zhan Gao, Huiwen Wang, Yaqing Liu, Cheng Guo, Yuanjiang Pan
Summary: Oligosaccharides play a crucial role in biological functions, and accurately identifying their structures is essential for a comprehensive understanding of their biological functions. This study successfully developed a nano-composite material that significantly improved the ionization efficiency of oligosaccharides, allowing for the differentiation and quantification of oligosaccharide isomers.
ANALYTICA CHIMICA ACTA
(2022)
Article
Chemistry, Multidisciplinary
Xiaowei Song, Qingce Zang, Chao Li, Tianhao Zhou, Richard N. N. Zare
Summary: We developed an immunoassay-based desorption electrospray ionization mass spectrometry imaging (immuno-DESI-MSI) technique for visualizing functional macromolecules. Boronic acid mass tags (BMTs) were synthesized to label antibodies as MSI probes, which can be released from the antibody by cleaving the boronic ester bond under acidic conditions. The BMTs can work in both optical and MS imaging modes and can be readily identified due to the introduction of the boron element.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Sangwon Cha, Gyouwoong Jun, Yougyeong Park, Sung Jun An, Donghoon Lee
Summary: Nanospray desorption electrospray ionization (nano-DESI) was used to analyze the metabolite fingerprints on Hypericum leaves. The intensity changes of key metabolites over time were observed through full mass scan experiments and monitored using selected ion monitoring and pseudo-selected reaction monitoring experiments. The correlation between the time-dependent changes in the metabolite fingerprints and depth-wise metabolite distribution was examined by removing the surface layers of the leaves multiple times.
Article
Allergy
Veronika Kanderova, Tamara Svobodova, Simon Borna, Martina Fejtkova, Vendula Martinu, Jana Paderova, Michael Svaton, Jarmila Kralova, Eva Fronkova, Adam Klocperk, Stepanka Pruhova, Min Ae Lee-Kirsch, Ludmila Hornofova, Miroslav Koblizek, Petr Novak, Olga Zimmermannova, Zuzana Parackova, Anna Sediva, Tomas Kalina, Ales Janda, Jana Kayserova, Marcela Dvorakova, Milan Macek, Petr Pohunek, Petr Sedlacek, Ashleigh Poh, Matthias Ernst, Tomas Brdicka, Ondrej Hrusak, Jan Lebl
Summary: This article reports a new monogenic autoinflammatory disorder caused by a de novo activating mutation in the HCK gene, characterized by cutaneous vasculitis and chronic pulmonary inflammation. The study shows the aberrant functions of mutant HCK and the therapeutic efficacy of the Janus kinase 1/2 inhibitor Ruxolitinib in treating inflammatory lung disease.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Chemistry, Analytical
Marek Polak, Ghazaleh Yassaghi, Daniel Kavan, Frantisek Filandr, Jan Fiala, Zdenek Kukacka, Petr Halada, Dmitry S. Loginov, Petr Novak
Summary: The combination of covalent labeling techniques with mass spectrometry is a progressive approach for studying protein surfaces and protein-ligand interactions. In this study, the interaction interface between the DNA binding domain of the FOXO4 protein and the DNA binding element was mapped. Different approaches were used to confirm the results and compare with other studies, showing consistent findings. This method is important for understanding the structure and dynamics of protein-DNA interactions.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Ghazaleh Yassaghi, Zdenek Kukacka, Jan Fiala, Daniel Kavan, Petr Halada, Michael Volny, Petr Novak
Summary: Fast photochemical oxidation of proteins (FPOP) footprinting is a method that uses chemical reactions to label protein structures. It provides information about protein conformation, dynamics, and interactions. FPOP samples can be analyzed using either bottom-up or top-down mass spectrometry approaches. The top-down approach allows for more specific selection of protein subpopulations, but is limited to smaller proteins. Comparison with bottom-up data confirms the usefulness of the top-down approach in oxidative protein footprinting.
ANALYTICAL CHEMISTRY
(2022)
Article
Cell Biology
Andi Alijagic, Nikolai Scherbak, Oleksandr Kotlyar, Patrik Karlsson, Xuying Wang, Inger Odnevall, Oldrich Benada, Ali Amiryousefi, Lena Andersson, Alexander Persson, Jenny Felth, Henrik Andersson, Maria Larsson, Alexander Hedbrant, Samira Salihovic, Tuulia Hyoetylaeinen, Dirk Repsilber, Eva Saerndahl, Magnus Engwall
Summary: The physicochemical characterization of AMPs revealed their complexity in size, shape, and chemistry. The AMPs exhibited concentration-dependent effects on the cytoskeleton, mitochondria, and cell membranes. Metabolomics and lipidomics analysis provided insight into the inflammation-related metabolites and extensive membrane remodeling induced by AMPs. Overall, AMP exposure resulted in internalization, oxidative stress, cytoskeleton disruption, mitochondrial activation, membrane remodeling, and metabolic reprogramming of lung epithelial cells and macrophages. Integrating Cell Painting with metabolomics and lipidomics offers an advanced nanosafety methodology to capture cellular and molecular phenotypes and understand the biological mechanisms of (nano)particle exposure.
Letter
Hematology
Natividad Alquezar-Artieda, Daniela Kuzilkova, Jennie Roberts, Katerina Hlozkova, Alena Pecinova, Petr Pecina, Martina Zwyrtkova, Eliska Potuckova, Daniel Kavan, Ivana Hermanova, Marketa Zaliova, Petr Novak, Tomas Mracek, Lucie Sramkova, Daniel A. Tennant, Jan Trka, Julia Starkova
Article
Microbiology
Jan Bavlovic, Ivona Pavkova, Lucie Balonova, Oldrich Benada, Jiri Stulik, Jana Klimentova
Summary: Francisella tularensis is a highly infectious bacterium that causes tularemia. Bacterial outer membrane vesicles (OMVs) of Francisella play a role in host-pathogen interactions and have potential use in a subunit vaccine. This study focused on the secretion of OMVs in O-antigen mutant strains and found that the presence of LPS and the O-antigen capsule is critical for the virulence and tubular shape of OMVs.
MICROBIOLOGICAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
Pieter-Jan Vermeire, Anastasia V. Lilina, Hani M. Hashim, Lada Dlabolova, Jan Fiala, Steven Beelen, Zdenek Kukacka, Jeremy N. Harvey, Petr Novak, Sergei V. Strelkov
Summary: Intermediate filaments (IFs) are essential components of the metazoan cytoskeleton and can self-assemble from soluble tetrameric species into typical 10-12 nm wide filaments. The molecular structure of mature IFs is poorly understood, but this study reveals that the formation of tetramers is dependent on the presence of the coil1A domain and is synergistically stabilized by interactions between coil1B domains, coil1A, coil2, and the head and rod domains. Additionally, small-angle X-ray scattering experiments show that elongated A(11) tetramers are dominant in low ionic strength solutions with structural flexibility in the terminal domains.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Josef Dvorak, Jana Novakova, Lucie Kraftova, Vendula Studentova, Martin Matejovic, Jaroslav Radej, Thomas Karvunidis, Jan Horak, Marcela Kralovcova, Jaroslav Hrabak, Zuzana Kalaninova, Michael Volny, Petr Novak, Petr Pompach
Summary: A rapid PCT detection method using MALDI-TOF mass spectrometry was developed and validated against LC-MS bottom-up workflow. The new method detects intact PCT and uncovers its alterations in septic patients' serum.
CLINICAL PROTEOMICS
(2023)
Article
Ecology
Brennen Heames, Filip Buchel, Margaux Aubel, Vyacheslav Tretyachenko, Dmitry Loginov, Petr Novak, Andreas Lange, Erich Bornberg-Bauer, Klara Hlouchova
Summary: A comparison between de novo genes and synthetic random sequences reveals no difference in biophysical properties, but in vitro expression demonstrates de novo proteins' higher solubility, indicating their better integration into the cellular system. The emergence of de novo genes provides a pathway for the formation of new proteins from previously non-coding DNA. While the likelihood of assuming a soluble and stable tertiary structure in de novo proteins remains unclear, evidence suggests that native-like biophysical properties are abundant in sequence space. Experimental characterization of putative de novo proteins in human and fly shows that their solubility and structure propensity are moderately higher compared to synthetic random proteins. The DnaK chaperone system further enhances the solubility of de novo proteins. Therefore, de novo proteins may be better integrated into the cellular system than random sequences due to their higher solubility.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Chemistry, Analytical
Marek Polak, Michael Palasser, Alan Kadek, Daniel Kavan, Christopher A. Wootton, Marc-Andre Delsuc, Kathrin Breuker, Petr Novak, Maria A. van Agthoven
Summary: Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that uses modulation of precursor ion radii to show the fragmentation patterns of analytes. This study introduces quadrupolar detection in 2D MS and discusses its advantages, as well as adapts existing data processing techniques for accurate frequency-to-mass conversion. The method is applied to the top-down analysis of covalently labeled ubiquitin and the label-free relative quantification of biomolecule isoforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Vera Chvalova, Vignesh Venkadasubramanian, Zuzana Klimova, Jana Vojtova, Oldrich Benada, Ondrej Vanatko, Tomas Vomastek, Tomas Grousl
Summary: This study used CRISPR/Cas9 and siRNA to decrease the expression of RACK1 in MDCK epithelial cells and Rat2 fibroblasts. The depletion of RACK1 resulted in decreased cell proliferation, increased cell area and perimeter, and the appearance of large binucleated cells, indicating a defect in cell cycle progression. These findings demonstrate the essential role of RACK1 in both epithelial and mesenchymal cell lines.
EXPERIMENTAL CELL RESEARCH
(2023)
Article
Biochemical Research Methods
Thomas Lambert, Marius Gramlich, Luisa Stutzke, Luke Smith, Dingyu Deng, Philipp D. Kaiser, Ulrich Rothbauer, Justin L. P. Benesch, Cornelia Wagner, Maximiliane Koenig, Petr Pompach, Petr Novak, Anne Zeck, Kasper D. Rand
Summary: Protein glycosylation is a common protein modification, but determining the HDX of glycosylated protein segments has been challenging. In this study, we developed a column containing PNGase Rc that can be integrated into a conventional HDX-MS setup to improve glycoprotein analysis. The PNGase Rc column enables efficient online removal of N-linked glycans and determination of glycosylated regions' HDX in complex glycoproteins. We also demonstrated the column's use in mapping the binding epitope of a mAb to c-Met, a complex glycoprotein drug target. Overall, our work shows that HDX-MS with the integrated PNGase Rc column allows fast and efficient deglycosylation under harsh quench conditions and provides comprehensive analysis of complex glycoproteins.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Eliska Koutna, Vanda Lux, Tomas Kouba, Jana Skerlova, Jiri Novacek, Pavel Srb, Rozalie Hexnerova, Hana Svachova, Zdenek Kukacka, Petr Novak, Milan Fabry, Simon Poepsel, Vaclav Veverka
Summary: This study reports the ability of the PWWP domain of transcriptional coactivator LEDGF to bind to specific histone modifications and reveals the role of the intrinsically disordered region in nucleosome binding. The interplay between the H3K36 methylation reader and protein binding module of LEDGF facilitates productive transcription elongation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Tereza Jurikova, Hynek Macha, Vanda Lupjanova, Tomas Pluhacek, Helena Maresova, Barbora Papouskova, Dominika Luptakova, Rutuja H. Patil, Oldrich Benada, Michal Grulich, Andrea Palyzova
Summary: Pseudomonas aeruginosa is a significant pathogen in hospital-acquired infections, often collaborating with the opportunistic fungal pathogen Aspergillus fumigatus in respiratory infections. This study identifies a potential new biomarker, QS molecule portfolio, which affects virulence factor secretion and biofilm formation in P. aeruginosa. The study also demonstrates changes in QS molecule levels during the transition from planktonic to sessile cells and in co-cultures with A. fumigatus.
Article
Materials Science, Textiles
Michal Syrovy, Pavla Capkova, Petr Rysanek, Oldrich Benada, Monika Vostinakova
Summary: The manufacturing of membranes for CO2 capture is an important research topic. This study aims to achieve maximum CO2 sorption capacity while maintaining air permeability with minimal technological steps. Electrospun nanofibrous membranes PAN/TETA and PAN/TEPA were prepared using one-step technology and two different spinning conditions - needle spinning and wire spinning. The best result was obtained for wire spinning PAN_TEPA_2% with a CO2 sorption capacity of 11.7 +/- 1.3 cm(3)/g and air permeability of 53 +/- 5 L/m(2)/s, providing potential for practical use.
JOURNAL OF INDUSTRIAL TEXTILES
(2023)
