Article
Chemistry, Analytical
Janella Marie de Jesus, Catia Costa, Amy Burton, Vladimir Palitsin, Roger Webb, Adam Taylor, Chelsea Nikula, Alex Dexter, Firat Kaya, Mark Chambers, Veronique Dartois, Richard J. A. Goodwin, Josephine Bunch, Melanie J. Bailey
Summary: Elemental and molecular imaging are important in understanding disease pathogenesis, and performing sequential elemental and molecular imaging poses challenges and successes. While compromises may be involved, research shows that correlating sulfur, iron, and lipid markers in a single tissue section at the 50 μm scale is feasible with sequential DESI-ME imaging.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Harvey E. Johnston, Kranthikumar Yadav, Joanna M. Kirkpatrick, George S. Biggs, David Oxley, Holger B. Kramer, Rahul S. Samant
Summary: Complete and reproducible extraction of protein is crucial for proteome analysis. Solvent precipitation SP3 (SP4) is proposed as an alternative method, which captures protein aggregates by centrifugation instead of magnetism. SP4 provides equivalent or higher protein yields and improved reproducibility. It also recovers more low-solubility and transmembrane proteins, offering higher recovery rates.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Xiaolu Yu, Hongju He, Xuezhi Zhao, Guangmin Liu, Liping Hu, Bing Cheng, Yaqin Wang
Summary: The study compared and optimized three tissue disruption methods for sample preparation, revealing limitations in processing intact GSLs in different plant tissues under the same microwave conditions, yet achieving good recoveries through methanol extraction. It emphasized the necessity of heating extraction when extracting GSLs from frozen-fresh samples.
Review
Chemistry, Analytical
Joao Raul Belinato, Vinicius Ricardo Acquaro, Luciana Teresa Dias Cappelini, Fabio Augusto
Summary: The interest in bioactive compounds from microorganisms has increased since the first discovery, with microorganisms being a key source of biomolecules with diverse applications. While conventional sample preparation techniques are still widely used, microextraction techniques show promise in overcoming limitations and promoting a deeper understanding of complex systems and the discovery of new molecules.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Fujia Wang, Tim Veth, Marije Kuipers, Maarten Altelaar, Kelly E. Stecker
Summary: A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. The performance of the S-Trap protocol for phosphoproteomics studies is unclear, and the addition of phosphoric acid (PA) in the existing protocol is detrimental to downstream phosphopeptide enrichment. This study systematically evaluates the performance of the S-Trap digestion for proteomics and phosphoproteomics, and demonstrates that an optimized S-Trap approach, with trifluoroacetic acid substituted for PA, is a simple and effective method for phosphoproteomics sample preparation.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Fenglin Shen, Yueting Xiong, Lei Zhang, Hengchao Li, Huanhuan Zhao, Xiaohui Liu, Pengyuan Yang
Summary: A new rapid and simple sample preparation method was developed for serum proteomic studies, allowing for efficient identification of multiple proteins in under 2 hours. This method has the potential to accelerate biomarker discovery and clinical application in serum protein research.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
John B. Coulton, James L. Edwards
Summary: The sample preparation technique described in the study involves online filter-assisted electroporation-based cell lysis and chilled organic solvent extraction for rapid preparation of metabolomic samples from suspended cells. By using isotopically labeled internal standards and C-13-glucose labeling experiments, the method ensures enzymatic quenching and successful incorporation of C-13 into organic acid metabolites. Analysis by nano-reverse-phase liquid chromatography-mass spectrometry (nano-RP-LC-MS) demonstrates the effectiveness of the technique in studying metabolites such as itaconate.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Stephanie Biedka, Brigitte F. Schmidt, Nolan M. Frey, Sarah M. Boothman, Jonathan S. Minden, Amber Lucas
Summary: This study presents a new protein sample preparation method, ProMTag, which enables whole proteome capture, cleanup, and release of intact proteins, as well as generation of peptides for downstream analysis. The ProMTag workflow yields high percentages for both intact proteins and proteome digests, making it a versatile and high-quality approach for proteome sample preparation.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Physical
Daniela Torres-Diaz, Romain Basalgete, Mathieu Bertin, Jean-Hugues Fillion, Xavier Michaut, Lionel Amiaud, Anne Lafosse
Summary: Recent research has found that X-ray irradiation of interstellar ice analogues can induce molecule desorption, potentially explaining the presence of gaseous organics in the coldest regions of the interstellar medium, particularly in protoplanetary disks. The proposed desorption mechanism involves the Auger decay of excited molecules following soft X-ray absorption, known as X-ray induced electron-stimulated desorption (XESD). In this study, pure methanol (CH3OH) ices were irradiated with 505 eV electrons to simulate the Auger electrons, and desorption yields of various organic fragments were quantitatively determined by mass spectrometry, showing remarkable similarity to XESD values.
Article
Chemistry, Multidisciplinary
Oliver J. Hale, Helen J. Cooper
Summary: This study demonstrates a mass spectrometry analysis method for the direct analysis of intact oligomeric membrane proteins from tissue. By characterizing protein assembly directly from sheep eye lens sections without sample pre-treatment, our approach allows for simultaneous analysis of soluble protein assemblies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Valeria Springer, Yuye Zhou, Angela Y. Aguilera, Asa Emmer
Summary: This study reports the application of a novel hybrid platform composed of copper oxide particles (Cu2O PS) and low amounts of 2,5-dihydroxybenzoic acid (DHB) in MALDI-MS. The combined Cu2O PS@DHB matrix allows for the analysis of intact proteins without surface modification of target plates, with good signal reproducibility. Additionally, the platform can be used for the analysis of glycopeptides in the low m/z range.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Bin Yan, Josephine Bunch
Summary: Native mass spectrometry allows for the study of intact proteins and their complexes, with the application of a specialized Waters DESI source and prototype spray emitter for rapid surface measurements of folded and native protein structures. Adding methanol to ammonium acetate solution in DESI spray solvent improves signal-to-noise ratio without compromising the preservation of folded protein structures. The optimized conditions enable the observation of folded protein ions with narrow charge state distribution and noncovalent-bond-assembled intact protein complexes.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
Tanja Bien, Sebastian Bessler, Klaus Dreisewerd, Jens Soltwisch
Summary: Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has the potential to visualize the spatial distribution of biomolecules in cell cultures and tissue sections with high resolution, but sample preparation is crucial. A study found that a robust sample preparation protocol can preserve cell morphology and molecular integrity, contributing to the study of cell-to-cell heterogeneities at a molecular level. Advancements in single-cell MALDI imaging could benefit from these protocols.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Lianlian Ma, Qingrong Xie, Mingyi Du, Yudi Huang, Yingying Chen, Dong Chen, Yizhu Xu, Hanhong Xu, Xinzhou Wu, Zhibin Yin
Summary: This study systematically investigated the optimized sample preparation conditions for insects and model organisms in mass spectrometry imaging (MSI), providing guidelines for MSI analysis and expanding its potential in life sciences and environmental sciences.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Chin-Wen Chen, Chia-Feng Tsai, Miao-Hsia Lin, Shu-Yu Lin, Chuan-Chih Hsu
Summary: Plant phosphoproteomics provides a global view of phosphorylation-mediated signaling in plants, but high-throughput methods with sensitive detection and accurate quantification are needed. In this study, we developed a tandem S-Trap-IMAC method based on suspension trapping, which improved the coverage and quantification accuracy of the Arabidopsis phosphoproteome compared to precipitation-based workflow. We applied this method to study ABA signaling in Arabidopsis seedlings and quantified key phosphorylation sites on core ABA signaling components across different time points, revealing the importance of multiply phosphorylated peptides in early ABA signaling. Our optimized workflow enables high-throughput phosphoproteome profiling of low-input plant samples.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Joaquim Torra, Celine Lafaye, Luca Signor, Sylvain Aumonier, Cristina Flors, Xiaokun Shu, Santi Nonell, Guillaume Gotthard, Antoine Royant
SCIENTIFIC REPORTS
(2019)
Article
Microbiology
Charlotte Lombardi, James Tolchard, Stephanie Bouillot, Luca Signor, Caroline Gebus, David Liebl, Daphna Fenel, Jean-Marie Teulon, Juliane Brock, Birgit Habenstein, Jean-Luc Pellequer, Eric Faudry, Antoine Loquet, Ina Attree, Andrea Dessen, Viviana Job
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Rita Puglisi, Elisabetta Boeri Erba, Annalisa Pastore
Article
Multidisciplinary Sciences
Guillaume Tetreau, Anne-Sophie Banneville, Elena A. Andreeva, Aaron S. Brewster, Mark S. Hunter, Raymond G. Sierra, Jean-Marie Teulon, Iris D. Young, Niamh Burke, Tilman A. Grunewald, Joel Beaudouin, Irina Snigireva, Maria Teresa Fernandez-Luna, Alister Burt, Hyun-Woo Park, Luca Signor, Jayesh A. Bafna, Rabia Sadir, Daphna Fenel, Elisabetta Boeri-Erba, Maria Bacia, Ninon Zala, Frederic Laporte, Laurence Despres, Martin Weik, Sebastien Boutet, Martin Rosenthal, Nicolas Coquelle, Manfred Burghammer, Duilio Cascio, Michael R. Sawaya, Mathias Winterhalter, Enrico Gratton, Irina Gutsche, Brian Federici, Jean-Luc Pellequer, Nicholas K. Sauter, Jacques-Philippe Colletier
NATURE COMMUNICATIONS
(2020)
Review
Biochemical Research Methods
Elisabetta Boeri Erba, Luca Signor, Carlo Petosa
JOURNAL OF PROTEOMICS
(2020)
Article
Multidisciplinary Sciences
Kim Krighaar Rasmussen, Andres Palencia, Anders K. Varming, Habiba El-Wali, Elisabetta Boeri Erba, Martin Blackledge, Karin Hammer, Torsten Herrmann, Mogens Kilstrup, Leila Lo Leggio, Malene Ringkjobing Jensen
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Guillaume Fouet, Isabelle Bally, Luca Signor, Katharina Haussermann, Nicole M. Thielens, Veronique Rossi, Christine Gaboriaud
Summary: C1q is a recognition protein of the classical complement pathway that can interact with multiple targets and initiate the complement cascade. This study reports the generation of the first recombinant form of human C1q without its recognition globular heads, retaining functional properties. By controlling the correct registering of collagen triple helices, the protein was correctly assembled and folded.
Article
Chemistry, Multidisciplinary
Gabriele Giachin, Matthew Jessop, Romain Bouverot, Samira Acajjaoui, Melissa Saidi, Anais Chretien, Maria Bacia-Verloop, Luca Signor, Philippe J. Mas, Adrien Favier, Eve Borel Meneroud, Michael Hons, Darren J. Hart, Eaazhisai Kandiah, Elisabetta Boeri Erba, Alain Buisson, Gordon Leonard, Irina Gutsche, Montserrat Soler-Lopez
Summary: ECSIT functions as the bridging node of the MCIA core complex, inducing the transformation of ACAD9 from a FAO enzyme to an MCIA factor, providing a unique molecular mechanism for coordinating the regulation of the FAO and OXPHOS pathways.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Luca Signor, Theo Paris, Caroline Mas, Adrien Picard, Georges Lutfalla, Elisabetta Boeri Erba, Laure Yatime
Summary: S100A9 and S100A8 are major constituents of the S100 family of calcium-binding proteins found exclusively in vertebrates; they can act as alarmins in response to pathological conditions and have antimicrobial properties mainly through metal sequestration. The crystal structures of S100A9 reveal a canonical homodimeric form and an intramolecular disulfide bridge that stabilizes the protein's conformation, shaping a second zinc-binding site per protomer. Calcium and zinc seem to affect the relative proportion of non-covalent and covalent homodimers of S100A9.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Joao Ramos, Valerie Laux, Michael Haertlein, Elisabetta Boeri Erba, Katherine E. McAuley, V. Trevor Forsyth, Estelle Mossou, Sine Larsen, Annette E. Langkilde
Summary: The study utilized a method to perdeuterate hen egg-white lysozyme, showing that different preparation methods have an impact on the thermal stability and enzymatic activity of the protein, potentially related to protein folding and deuteration effects.
Article
Chemistry, Multidisciplinary
Nicolas Duraffourg, Maxime Leprince, Serge Crouzy, Olivier Hamelin, Yves Usson, Luca Signor, Christine Cavazza, Vincent Forge, Luca Albertin
Summary: An artificial amyloid-based redox hydrogel was designed to mediate electron transfer between a [NiFeSe] hydrogenase and an electrode, resulting in bioelectrodes capable of catalytic oxidation of H-2. The hybrid redox protein self-assembled into nanofibrils with aligned redox groups, allowing for close encounters and immobilization of the hydrogenase at the surface of carbon electrodes under mild conditions. Catalytic current densities of up to 270 mu A cm(-2) with an overpotential of 0.33 V were achieved under quiescent conditions at 45 degrees C.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Romain Linares, Charles-Adrien Arnaud, Gregory Effantin, Claudine Darnault, Nathan Hugo Epalle, Elisabetta Boeri Erba, Guy Schoehn, Cecile Breyton
Summary: The structures of the T5 tail tip before and after interaction with its receptor, FhuA, have been determined using cryo-electron microscopy. These structures reveal important conformational changes, such as bending of the central fiber, anchoring of the tail to the membrane, opening of the tail tube, and formation of a transmembrane channel. This provides detailed insights into the initial steps of the infection mechanism.
Article
Biochemistry & Molecular Biology
Hamida Laroussi, Ariadna B. Juarez-Martinez, Aline Le Roy, Elisabetta Boeri Erba, Frank Gabel, Bernard de Massy, Jan Kadlec
Summary: Meiotic recombination in mice is initiated by DNA double-strand breaks (DSBs), catalyzed by the TOPOVIL complex. This complex's activity is regulated by meiotic factors such as REC114, MEI4, and IHO1, but the mechanism is not well understood. This study reveals the molecular details of these factors and their interactions, including REC114 forming homodimers, associating with MEI4 as a heterotrimer, and IHO1 forming tetramers. The study also shows that IHO1 directly interacts with REC114 and shares a binding surface with TOPOVIBL and another meiotic factor ANKRD31. These findings suggest the existence of a ternary IHO1-REC114-MEI4 complex and highlight the potential regulatory role of REC114 in mediating interactions with multiple partners.
Article
Multidisciplinary Sciences
Domenico Iuso, Isabel Garcia-Saez, Yohann Coute, Yoshiki Yamaryo-Botte, Elisabetta Boeri Erba, Annie Adrait, Nour Zeaiter, Malgorzata Tokarska-Schlattner, Zuzana Macek Jilkova, Faycal Boussouar, Sophie Barral, Luca Signor, Karine Couturier, Azadeh Hajmirza, Florent Chuffart, Ekaterina Bourova-Flin, Anne-Laure Vitte, Lisa Bargier, Denis Puthier, Thomas Decaens, Sophie Rousseaux, Cyrille Botte, Uwe Schlattner, Carlo Petosa, Saadi Khochbin
Summary: Nucleoside diphosphate kinases (NME1/2) regulate nucleotide homeostasis and bind to CoA. NME2 mediates gene transcription response in liver cells under high-fat diet, repressing fatty acid accumulation and activating protective gene expression program.