Article
Chemistry, Analytical
Xing-Cai Wang, Jia-Ni Zhang, Juan-Juan Zhao, Xiao-Meng Guo, Shu-Fang Li, Qing-Xia Zheng, Ping-Ping Liu, Peng Lu, Hai-Yan Fu, Yong-Jie Yu, Yuanbin She
Summary: In this study, a new platform called AntDAS-DDA was developed for the automatic processing of UHPLC-HRMS data sets acquired under the DDA mode. The platform includes several algorithms for feature extraction, MS/MS spectrum construction, and compound identification. Results showed that AntDAS-DDA can effectively extract features in complex sample matrices and improve compound identification efficiency by about 20%. Comparison with other advanced data analysis tools indicated that AntDAS-DDA can be used as an alternative for routine UHPLC-HRMS-based untargeted metabolomics.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Charles N. Lowe, Kristin K. Isaacs, Andrew McEachran, Christopher M. Grulke, Jon R. Sobus, Elin M. Ulrich, Ann Richard, Alex Chao, John Wambaugh, Antony J. Williams
Summary: With the increasing availability of high-resolution mass spectrometers, suspect screening and non-targeted analysis have become popular compound identification tools for environmental researchers. Using a chromatography method to separate chemicals before injecting them into the mass spectrometer, different compounds can be observed based on the type of instrument used. This study utilized experimental datasets to predict the amenability of chemical compounds to detection with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS).
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Chaoying Zhang, Zengnan Wu, Xinchang Gao, Xia Wang, Haifang Li, Jin-Ming Lin
Summary: This study proposes a noninterference ion addition (NIA) method by electrolysis to improve homogeneous crystallization during the evaporation process of sample droplets on the target plate, thus improving the quantitative detection of bacteria using MALDI-TOF MS. By inserting an active metal wire as the anode electrode in the droplet and releasing metal ions through electrolysis, the directional migration of metal ions under the electric field can hinder the migration of matrix molecules and homogenize the matrix crystals. Simultaneously, trace cationic surfactant is added to the droplet for pinning the contact surface to define the circular crystallization region. Metal ions from the anode electrode wire are deposited on the surface of the target plates, serving as the cathode, and do not interfere with ionization during MALDI-MS detection. This NIA method benefits homogeneous crystallization and improves quantitative analysis, making it suitable for biological samples with different matrices and allowing for quantitative analysis of bacterial samples.
ANALYTICAL CHEMISTRY
(2023)
Article
Food Science & Technology
Aurelien Cuchet, Anthony Anchisi, Philippe Telouk, Yijiao Yao, Frederic Schiets, Francois Fourel, Yohann Clement, Pierre Lanteri, Elise Carenini, Patrick Jame, Herve Casabianca
Summary: A methodology for authentication of Allium species essential oils through multi element stable isotope analysis was developed, assessing the naturalness of the oils through compound specific 813C and 834S, with the use of chemometric models to evaluate purity.
Article
Food Science & Technology
Simon D. Kelly, Aiman Abrahim, Peter Rinke, Andrew Cannavan
Summary: An improved procedure utilizing gas chromatography-isotope ratio mass spectrometry has successfully detected the addition of exogenous C4 plant-derived sugars to pineapple juice. Site-specific C-13 analysis of ethanol derived from pineapple sugars has proven to be a reliable method in differentiating between authentic pineapple juices and those adulterated with commercial beet and cane sucrose.
NPJ SCIENCE OF FOOD
(2021)
Article
Chemistry, Multidisciplinary
Hilda Sandstrom, Matti Rissanen, Juho Rousu, Patrick Rinke
Summary: This article provides an overview of the current state of data-driven compound identification with mass spectrometry in atmospheric science. It discusses the challenges and future steps towards a digital era in atmospheric mass spectrometry. Enhancing atmospheric compound identification is crucial for understanding atmospheric processes, and mass spectrometry enables fast and accurate identification in both field and laboratory settings. Digitizing identification protocols may expedite new compound discovery, but it requires relevant reference standards and the establishment of a collaborative, open data infrastructure.
Article
Chemistry, Analytical
Huaxu Yu, Peijun Sang, Tao Huan
Summary: The normality of metabolomic data is crucial for statistical analyses, but research on the distribution of metabolomic data is rare. In this study, a comprehensive investigation of metabolomic data distributions was conducted using large-scale datasets. It was found that metabolic features exhibit diverse distribution types that cannot be properly normalized using conventional transformation algorithms. To address this, an adaptive Box-Cox (ABC) transformation, which can improve data normality for various distribution types, was proposed. The ABC transformation showed excellent performance in normalizing skewed metabolomic data, outperforming conventional approaches in simulations and real metabolomic studies.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Katherine T. Peter, Allison L. Phillips, Ann M. Knolhoff, Piero R. Gardinali, Carlos A. Manzano, Kelsey E. Miller, Manuel Pristner, Lyne Sabourin, Mark W. Sumarah, Benedikt Warth, Jon R. Sobus
Summary: Non-targeted analysis (NTA) workflows using mass spectrometry are becoming increasingly popular in various disciplines, but there is still a lack of universally accepted reporting standards. To address this issue, researchers have developed the NTA Study Reporting Tool (SRT), which has been shown to be effective in guiding study design, manuscript writing, and evaluating NTA reporting quality through analysis of published articles.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Applied
Huizhen Wu, Zhi Liu, Hu Zhang, Shuangnan Xie, Chao Tang, Wei Liu, Bin Li, Piao Chen, Zihong Zhang, Mingrong Qian
Summary: In this study, a method using GC-C-IRMS analysis and pre-column derivatization was developed to determine the 815N stable ratio of SEM in shrimp and crab. The results showed that the 815N values of SEM significantly decreased after the use of nitrofurazone. Furthermore, the analysis of SEM in crustaceans indicated a significant difference between SEMex and SEMend, which can be used for determining the source of SEM in vivo.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2023)
Article
Chemistry, Analytical
Yuxin An, Qun Zhao, Hang Gao, Lili Zhao, Xiao Li, Xiaodan Zhang, Zhen Liang, Lihua Zhang, Yukui Zhang
Summary: Chemical crosslinking combined with mass spectrometry (CXMS) is a powerful method for global characterization of protein complexes. In this study, we proposed a strategy called MoTE to selectively remove unhydrolyzed monolinked peptides and enrich crosslinked peptides for regular peptide removal.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemical Research Methods
Christoph A. Krettler, Gerhard G. Thallinger
Summary: Metabolomics and lipidomics play significant roles in personalized medicine, but data analysis remains a bottleneck. Recent research utilizing computational methods and simulating mass spectra has made valuable progress in annotating experimental data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Analytical
Ziyun Xu, Hamza Chughtai, Lei Tian, Lan Liu, Jean-Francois Roy, Stephane Bayen
Summary: In this study, QSRR models were developed to predict the chromatographic retention time of chemicals and identify leachables from plastic packaging samples. The models showed better predictive capacities compared to linear models, and analyzing a sample on multiple chromatographic columns increased the ability to filter false positives.
Article
Agriculture, Dairy & Animal Science
Katarzyna Pluta, Peter R. H. Jones, Natalia Drabinska, Norman Ratcliffe, Stephen D. Carrington, Patrick Lonergan, Alexander C. O. Evans
Summary: This study identified volatile organic compounds (VOC) in bovine cervicovaginal mucus that could be potential biomarkers of estrus and ovulation. The results may contribute to the development of a sensor device based on VOC for detecting estrus and ovulation in cattle, particularly in the dairy industry where most females are bred by artificial insemination. The VOC identified in mucus samples included 2-butanone, acetone, 2-pentanone, 4-methyl-2-pentanone, 1-(1-methylethoxy)-2-propanone, ethanol, 2-methyl-2-propanol, and 2-butanol.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Chemistry, Analytical
Fei Wang, Jaanus Liigand, Siyang Tian, David Arndt, Russell Greiner, David S. Wishart
Summary: Mass spectrometry (MS) is commonly used in metabolomics for identifying and annotating metabolites. CFM-ID is a computer program that accurately predicts EST-MS/MS spectrum for a given compound structure, improving compound-to-mass-spectrum prediction and in silico mass-spectrum-to-compound identification. This new version of CFM-ID (version 4.0) demonstrates significantly increased accuracy in both ET-MS/MS spectral prediction and compound identification.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Seongho Kim, Ikuko Kato, Xiang Zhang
Summary: Compound identification is a critical step in untargeted metabolomics. This study evaluates the performance of 15 binary similarity measures for compound identification and identifies the best performing measures.
Article
Chemistry, Applied
Ana Edileia Barbosa Pereira Leal, Ana Paula de Oliveira, Raira Feitosa dos Santos, Juliana Mikaelly Dias Soares, Erica Martins de Lavor, Michelle Cruz Pontes, Julianeli Tolentino de Lima, Alan Diego da Conceicao Santos, Jose Carlos Tomaz, Gibson Gomes de Oliveira, Fausto Carnevale Neto, Norberto Peporine Lopes, Larissa Araujo Rolim, Jackson Roberto Guedes da Silva Almeida
NATURAL PRODUCT RESEARCH
(2020)
Article
Biochemical Research Methods
Fausto Carnevale Neto, Marcio Adriano Andreo, Daniel Raftery, Joao Luis Callegari Lopes, Norberto Peporine Lopes, Ian Castro-Gamboa, Beatriz Helena Lameiro de Noronha Sales Maia, Emmanoel Vilaca Costa, Ricardo Vessecchi
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2020)
Article
Cardiac & Cardiovascular Systems
Julia Ritterhoff, Sara Young, Outi Villet, Dan Shao, F. Carnevale Neto, Lisa F. Bettcher, Yun-Wei A. Hsu, Stephen C. Kolwicz, Daniel Raftery, Rong Tian
CIRCULATION RESEARCH
(2020)
Article
Clinical Neurology
Eeeseung Byun, Susan M. McCurry, Mark Opp, Dongqi Liu, Kyra J. Becker, Hilaire J. Thompson
JOURNAL OF CLINICAL NEUROSCIENCE
(2020)
Letter
Biochemical Research Methods
Fausto Carnevale Neto, Thais Guaratini, Pio Colepicolo, Paul J. Gates, Norberto Peporine Lopes
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2020)
Article
Nursing
Kendra J. Kamp, Claire Han, Robert J. Shulman, Kevin C. Cain, Pamela Barney, Mark R. Opp, Lin Chang, Robert L. Burr, Margaret M. Heitkemper
Summary: This study found no significant differences in plasma or stimulated cytokine levels between women with IBS and healthy controls. Women who did not use hormonal contraceptives had higher levels of IL-1 beta and TNF-alpha. Among women with IBS, there were significant correlations between daily psychological distress and certain cytokine levels. Further research is needed to explore the impact of hormonal contraceptive use on innate immune activation among women with IBS.
BIOLOGICAL RESEARCH FOR NURSING
(2021)
Article
Nutrition & Dietetics
Sandi L. Navarro, Lisa Levy, Keith R. Curtis, Isaac Elkon, Orsalem J. Kahsai, Hamza S. Ammar, Timothy W. Randolph, Natalie N. Hong, Fausto Carnevale Neto, Daniel Raftery, Robert S. Chapkin, Johanna W. Lampe, Meredith A. J. Hullar
Article
Critical Care Medicine
Dara L. Horn, Lisa F. Bettcher, Sandi L. Navarro, Vadim Pascua, Fausto Carnevale Neto, Joseph Cuschieri, Daniel Raftery, Grant E. O'Keefe
Summary: The study found that metabolic profiles differ between trauma victims who ultimately die or develop CCI, and those who recover rapidly. Differences were observed in markers of inflammation, oxidative stress, amino acid metabolism, and alterations in the gut microbiome. Targeted metabolomics has the potential for early diagnosis and intervention post-injury.
JOURNAL OF TRAUMA AND ACUTE CARE SURGERY
(2021)
Article
Cell Biology
Claudio de Lucia, Michela Piedepalumbo, Lu Wang, Fausto Carnevale Neto, Daniel Raftery, Erhe Gao, Domenico Pratico, Daniel E. L. Promislow, Walter J. Koch
Summary: This study aimed to evaluate the effects of aging and ischemia/reperfusion injury on plasma metabolomic profiling in mice. The results showed that aging significantly affects circulating metabolite levels, while ischemic injury did not have a drastic impact on LV function in aged mice compared to young mice.
Article
Genetics & Heredity
Kathryn A. Jewett, Ruth E. Thomas, Chi Q. Phan, Bernice Lin, Gillian Milstein, Selina Yu, Lisa F. Bettcher, Fausto Carnevale Neto, Danijel Djukovic, Daniel Raftery, Leo J. Pallanck, Marie Y. Davis
Summary: This study shows that GCase deficiency leads to abnormal protein aggregation within EVs, and restoring GCase protein reduces protein aggregation and affects the spread of protein aggregation between tissues. These findings are important for understanding PD progression and may lead to new targets for slowing neurodegeneration.
Article
Chemistry, Analytical
Fausto Carnevale Neto, Daniel Raftery
Summary: This study utilized tandem MS-based enhanced molecular networks to improve metabolite annotation in urine extracts, achieving a high success rate in annotation. By integrating methods such as unsupervised substructure discovery, the chemical characterization of compounds was expanded to nearly 50% of the data set successfully.
ANALYTICAL CHEMISTRY
(2021)
Letter
Biochemical Research Methods
Fausto Carnevale Neto, Vadim Pascua, Daniel Raftery
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2021)
Article
Plant Sciences
Fausto Carnevale Neto, Trevor N. Clark, Norberto P. Lopes, Roger G. Linington
Summary: This study integrated ion mobility spectrometry (IMS) into a liquid chromatography-mass spectrometry (LC-MS2) platform for the characterization of natural product mixtures. The results showed that integrating IMS improved metabolite detection and the quality of MS2 spectra.
JOURNAL OF NATURAL PRODUCTS
(2022)
Article
Biology
Rachel K. Rowe, Tabitha R. F. Green, Katherine R. Giordano, J. Bryce Ortiz, Sean M. Murphy, Mark R. Opp
Summary: Microglia are found to play a critical role in regulating sleep after an immune challenge. Depletion of microglia results in increased sleep following an inflammatory injection, while repopulation of microglia leads to changes in sleep patterns. This study suggests that microglia are necessary for sleep regulation after inflammation.
Review
Chemistry, Multidisciplinary
Alan C. Pilon, Denise M. Selegato, Richard P. Fernandes, Paula C. P. Bueno, Danielle R. Pinho, Fausto Carnevale Neto, Rafael T. Freire, Ian Castro-Gamboa, Vanderlan S. Bolzani, Norberto P. Lopes