Article
Biochemistry & Molecular Biology
Francisco Traquete, Joao Luz, Carlos Cordeiro, Marta Sousa Silva, Antonio E. N. Ferreira
Summary: Untargeted metabolomics aims to identify and quantify most metabolites in a biological system. Mass spectrometry-based analysis can generate mass-difference networks, which can be used for ranking chemical transformations and classifying metabolic profiles.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Plant Sciences
Hayden E. Hodges, Heather J. Walker, Aaron J. Cowieson, Robert J. Falconer, Duncan D. Cameron
Summary: Modern feed quality sorghum grain has been bred to reduce anti-nutrients, but its inclusion in monogastric animal diets can still result in variable performance. Sorghum grain contains several negative intrinsic factors which may be responsible for muted feed performances. FT-IR and mass spectrometry can be used to discriminate among different sorghum varieties, and could be incorporated into quality control applications.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Analytical
Valentina Calabrese, Isabelle Schmitz-Afonso, Wassila Riah-Anglet, Isabelle Trinsoutrot-Gattin, Barbara Pawlak, Carlos Afonso
Summary: In this study, the performance of direct introduction electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) coupled with Fourier-Transform ion cyclotron resonance mass spectrometry (FTICR MS) for analyzing root exudates (RE) was systematically evaluated. MALDI showed better salt tolerance and ionization efficiency at high salinity, making it suitable for analyzing metabolites in complex matrices. The study also demonstrated the complementarity of the two ionization sources and the advantage of MALDI in detecting metabolites suffering from matrix effects in ESI mode.
Article
Multidisciplinary Sciences
Nicholas J. J. Morehouse, Trevor N. N. Clark, Emily J. J. McMann, Jeffrey A. A. van Santen, F. P. Jake Haeckl, Christopher A. A. Gray, Roger G. G. Linington
Summary: Spectral matching of MS2 fragmentation spectra has limitations due to instrument differences and limited spectral reference libraries. To overcome this challenge, SNAP-MS uses structural similarity network annotation to assign compound families to molecular networking subnetworks without using experimental or calculated reference spectra. SNAP-MS accurately annotates subnetworks built from both reference spectra and an in-house microbial extract library, and predicts compound families from published molecular networks acquired using different MS instruments.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Francisco Traquete, Joao Luz, Carlos Cordeiro, Marta Sousa Silva, Antonio E. N. Ferreira
Summary: Metabolomics aims to identify and quantify small molecules in biological systems using high-resolution methods, with suitable data preprocessing being fundamental. The traditional data analysis focuses on comparison of feature intensity values, while the new pre-treatment method Binary Simplification encoding (BinSim) can effectively simplify metabolomics data analysis pipelines.
Article
Biochemistry & Molecular Biology
Maria Pilar Giner, Stefan Christen, Simona Bartova, Mikhail Makarov, Marie E. Migaud, Carles Canto, Sofia Moco
Summary: NAD(+) and its reduced form NADH are essential coenzymes in hundreds of metabolic reactions, serving as substrates for key enzymes. Analyzing the NAD(+) metabolome using liquid chromatography-tandem mass spectrometry can provide insights into NAD(+) biology and its implications for health and disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Chiara Maria Vitale, Arjen Lommen, Carolin Huber, Kevin Wagner, Borja Garlito Molina, Rosalie Nijssen, Elliott James Price, Marco Blokland, Frederike van Tricht, Hans G. J. Mol, Martin Krauss, Laurent Debrauwer, Olga Pardo, Nuria Leon, Jana Klanova, Jean-Philippe Antignac
Summary: A set of QA/QC criteria for nontargeted measurement of pesticide exposure markers in human urine has been proposed and applied in the HBM4EU project. The criteria include monitoring signal intensities, mass accuracy, and retention times of selected markers. The results show high repeatability and accuracy of the data. This is the first time that harmonized QA/QC criteria have been used to assess the quality of nontargeted analysis of human samples across multiple laboratories.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Daniel Eilertz, Michael Mitterer, Joerg M. Buescher
Summary: This study presents an automated tool automRm for preprocessing of liquid chromatography-mass spectrometry data, which includes features such as using machine learning for chromatographic peak detection and quality control of results. The tool is generally applicable to a wide range of analytical methods and outperforms other software solutions when applied to a HILIC-MS data set.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Jacob W. McCabe, Benjamin J. Jones, Thomas E. Walker, Robert L. Schrader, Adam P. Huntley, Jixing Lyu, Nathan M. Hoffman, Gordon A. Anderson, Peter T. A. Reilly, Arthur Laganowsky, Vicki H. Wysocki, David H. Russell
Summary: This study presents a digital-waveform dual-quadrupole mass spectrometer to improve the performance of a drift tube FT-IMS high-resolution Orbitrap mass spectrometer in studying large proteins and protein complexes. The dual-quadrupole analyzer allows for low-energy collisional activation of ions and precise mass selection using digital-waveform technology, enhancing the capabilities of the instrument at a lower cost compared to traditional RF drivers.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
Teresa S. McMillen, Andrew Leslie, Kenneth Chisholm, Susanne Penny, Jeffrey Gallant, Alejandro Cohen, Arik Drucker, James P. Fawcett, Devanand M. Pinto
Summary: This study presents a comprehensive and quantitatively robust method for metabolomic analysis, using HILIC and RP stationary phases combined with positive and negative electrospray ionization. The method allows for complete analysis of a single sample in as little as 40 minutes and has been validated with clinical samples.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Yanlong Zhu, Benjamin Wancewicz, Michael Schaid, Timothy N. Tiambeng, Kent Wenger, Yutong Jin, Heino Heyman, Christopher J. Thompson, Aiko Barsch, Elizabeth D. Cox, Dawn B. Davis, Allan R. Brasier, Michelle E. Kimple, Ying Ge
Summary: Metabolomics is increasingly recognized as a preferred method for understanding biological systems' responses to stress, and utilizing FIE-FTICR MS technology allows for efficient analysis of different metabolite features in plasma samples with high reproducibility.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Elvin R. Cabrera, Brian H. Clowers
Summary: By casting ion population's mobility information in the frequency domain, time-dispersive ion mobility techniques can now be compatible with slower mass analyzers like ion traps. Recent progress has been made in maximizing the efficiency of Fourier transform ion mobility-mass spectrometry (FT-IM-MS) experiments, but the intersection between practical implementation considerations and theoretical limits of traditional signal processing techniques needs to be further explored. The importance of avoiding signal aliasing due to undersampling signals, along with evaluating limitations imposed by experimental parameters, is crucial for successful Fourier-based multiplexing experiments.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
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
Elvin R. Cabrera, Brian H. Clowers
Summary: This study describes a method of modulating the ion gates of ion mobility spectrometry using a discrete stepwise function, achieving synchronization between the generated frequencies and the scan rate of the linear ion trap. This method eliminates the ambiguity of assigning the ion current derived from a single modulation frequency and maintains high levels of precision across different combinations.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
Tusharkanti Ghosh, Daisy Philtron, Weiming Zhang, Katerina Kechris, Debashis Ghosh
Summary: The MaRR procedure was introduced to examine reproducibility in mass spectrometry-based metabolomics experiments, showing higher reproducibility for technical replicates compared to biological replicates across different datasets. The MaRR procedure tends to have high power for detecting reproducible metabolites in most situations, while in some cases it may perform less well.
BMC BIOINFORMATICS
(2021)
Article
Agronomy
Lucy Alford, Richard Marley, Anthony Dornan, Jean-Sebastien Pierre, Julian A. T. Dow, Ronald J. Nachman, Shireen A. Davies
PEST MANAGEMENT SCIENCE
(2019)
Article
Developmental Biology
Guillermo Martinez-Corrales, Pablo Cabrero, Julian A. T. Dow, Selim Terhzaz, Shireen-A. Davies
Article
Biochemistry & Molecular Biology
Aniruddha A. Pandit, Shireen-Anne Davies, Guy Smagghe, Julian A. T. Dow
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2019)
Article
Genetics & Heredity
Erez Cohen, Jessica K. Sawyer, Nora G. Peterson, Julian A. T. Dow, Donald T. Fox
Editorial Material
Biology
Michael H. Dickinson, Leslie B. Vosshall, Julian A. T. Dow
JOURNAL OF EXPERIMENTAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Pablo Cabrero, Selim Terhzaz, Anthony J. Dornan, Saurav Ghimire, Heather L. Holmes, Daniel R. Turin, Michael F. Romero, Shireen A. Davies, Julian A. T. Dow
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Julian A. T. Dow, Sue Ann Krause, Pawel Herzyk
Summary: The Malpighian tubule is capable of transporting fluid at remarkable rates, with recent focus on understanding the mechanisms behind achieving and controlling these high rates, particularly in the Drosophila tubules. Specialized cell types with active cation transport in principal cells and chloride and water shunts in intercalated stellate cells contribute to achieve net fluid secretion. Genes underlying these processes have been identified and localized within the tubule, and the upcoming post-genomic data is expected to bring new discoveries in this field.
CURRENT OPINION IN INSECT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Takashi Koyama, Selim Terhzaz, Muhammad T. Naseem, Stanislav Nagy, Kim Rewitz, Julian A. T. Dow, Shireen A. Davies, Kenneth Halberg
Summary: Neurosecretory cells in Drosophila release Capa hormones in response to nutrient levels, activating the Capa receptor in peripheral tissues to regulate energy homeostasis. Disruption of Capa/CapaR signaling leads to intestinal hypomotility and impaired nutrient absorption, depleting internal nutrient stores. Additionally, Capa/CapaR inhibits the release of a hormone that mobilizes energy from adipose tissue to prevent harmful hyperglycemia.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Sue A. Krause, Gayle Overend, Julian A. T. Dow, David P. Leader
Summary: FlyAtlas 2 is a database and web application for studying gene expression in different tissues of Drosophila melanogaster, with enhancements including a 'Profile' search function and a dedicated feature for exploring gene expression in the larval midgut. The database now includes data from 13 tissues, five sex-specific tissues, and eight larval tissues, with major improvements to the interface.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Urology & Nephrology
Julian A. T. Dow, Matias Simons, Michael F. Romero
Summary: The fruitfly Drosophila melanogaster serves as a suitable and cost-effective model for studying kidney diseases. It has advantages such as easy maintenance, availability of genetic mutants and powerful transgenic technologies. Various tissues in Drosophila melanogaster are involved in renal and excretory functions, allowing investigation of epithelial transport, kidney stone formation, and diseases associated with specific genes. The fly model provides insights into the mechanisms of kidney disease.
NATURE REVIEWS NEPHROLOGY
(2022)
Article
Multidisciplinary Sciences
Hongjie Li, Jasper Janssens, Maxime De Waegeneer, Sai Saroja Kolluru, Kristofer Davie, Vincent Gardeux, Wouter Saelens, Fabrice David, Maria Brbic, Jure Leskovec, Colleen N. McLaughlin, Qijing Xie, Robert C. Jones, Katja Brueckner, Jiwon Shim, Sudhir Gopal Tattikota, Frank Schnorrer, Katja Rust, Todd G. Nystul, Zita Carvalho-Santos, Carlos Ribeiro, Soumitra Pal, Sharvani Mahadevaraju, Teresa M. Przytycka, Aaron M. Allen, Stephen F. Goodwin, Cameron W. Berry, Margaret T. Fuller, Helen White-Cooper, Erika L. Matunis, Stephen DiNardo, Anthony Galenza, Lucy Erin O'Brien, Julian A. T. Dow, Heinrich Jasper, Brian Oliver, Norbert Perrimon, Bart Deplancke, Stephen R. Quake, Liqun Luo, Stein Aerts
Summary: This study presents a single-cell atlas of the fruit fly Drosophila melanogaster, including 580,000 nuclei and annotations of over 250 distinct cell types. It serves as a valuable resource for the Drosophila community and provides a reference for studying genetic perturbations and disease models at single-cell resolution.
Article
Cell Biology
Anthony J. Dornan, Kenneth Halberg, Liesa-Kristin Beuter, Shireen-Anne Davies, Julian A. T. Dow
Summary: This study found that the secretion capacity of Drosophila renal tubules declines with age, accompanied by mislocalisation of septate junction (SJ) proteins and progressive degeneration in cellular morphology. Acute loss of the SJ protein Snakeskin in adult tubules leads to changes in cellular and tissue structure, loss of cell polarity and barrier integrity. These findings demonstrate an important link between homeostasis and organismal viability, and provide new insights into the mechanisms underlying ageing and renal disease.
JOURNAL OF CELL SCIENCE
(2023)
Correction
Urology & Nephrology
Julian A. T. Dow, Matias Simons, Michael F. Romero
NATURE REVIEWS NEPHROLOGY
(2023)
Article
Physiology
Saurav Ghimire, Selim Terhzaz, Pablo Cabrero, Michael F. Romero, Shireen A. Davies, Julian A. T. Dow
AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY
(2019)
Article
Physiology
Greg M. Landry, Eva Furrow, Heather L. Holmes, Taku Hirata, Akira Kato, Paige Williams, Kari Strohmaier, Chris J. R. Gallo, Minhwang Chang, Mukesh K. Pandey, Huailei Jiang, Aditya Bonsal, Marie-Christine Franz, Nicolas Montalbetti, Mariam P. Alexander, Pablo Cabrero, Julian A. T. Dow, Timothy R. DeGrado, Michael F. Romero
AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY
(2019)
