Article
Marine & Freshwater Biology
Eric Bollinger, Jochen P. Zubrod, Marco Konschak, Ralf Schulz, Mirco Bundschuh
Summary: Stable isotope analysis is an important technique in food web ecology, but its effectiveness can be unclear in complex systems. The use of heavy isotope tracers has been suggested as a way to enhance the utility of stable isotope analysis, but this study found that labeling could potentially affect isotopic fractionation and bias conclusions. While the physiological and activity levels of organisms in autotrophy-based and detritus-based aquatic food webs were not significantly affected by labeling, the study supported the isotopic redundancy hypothesis, which suggests that metabolic processes can be altered by discrete quantum mechanical states.
AQUATIC TOXICOLOGY
(2023)
Article
Biochemical Research Methods
Kosuke Ogata, Chia-Feng Tsai, Yasushi Ishihama
Summary: An improved workflow was established for highly sensitive multiplexed quantitative phosphoproteomics using a nanoscale solid-phase TMT labeling reactor. The optimized protocol allowed for quantifying selumetinib-regulated phosphorylated sites in HeLa proteins with a nearly 10-fold increase in sensitivity compared to conventional methods. Raw MS data files have been deposited and made publicly available for further analysis.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Analytical
Xiaoling Su, Deying Chen, Liang Li, Lanjuan Li
Summary: The study demonstrates that perfusion can significantly alter the liver metabolome, recommending the use of non-perfused liver for comprehensive liver metabolomics analysis for high coverage.
ANALYTICA CHIMICA ACTA
(2021)
Article
Pharmacology & Pharmacy
Sabrina Wohlfart, Michael Kilian, Philip Storck, Thomas Gutsmann, Klaus Brandenburg, Walter Mier
Summary: A novel method for precise quantification of Pep19-2.5 in biological samples has been developed in this study, which is crucial for the treatment of sepsis. The method utilizes mass spectrometry and labeled amino acid residues to reliably quantify the peptide content.
Article
Pharmacology & Pharmacy
Zhenpeng Zhang, Yao Zhang, Yuan Li, Songhao Jiang, Feng Xu, Kaixuan Li, Lei Chang, Huiying Gao, Predrag Kukic, Paul Lawford Carmichael, Mark Liddell, Jin Li, Qiang Zhang, Zhitang Lyu, Shuangqing Peng, Tao Zuo, Liz Tulum, Ping Xu
Summary: Protein phosphorylation is a common post-translational modification that plays an important role in regulating cell homeostasis. Quantitative phosphoproteomics can sensitively assess the effects of chemicals on cells, which is beneficial for developing non-animal approaches for chemical safety assessment.
TOXICOLOGY AND APPLIED PHARMACOLOGY
(2022)
Article
Chemistry, Analytical
Jihee Yun, Jae-Yoon Jo, Sami T. Tuomivaara, Jae-Min Lim
Summary: Robust mass spectrometry-based methods for quantitative glycomics rely heavily on stable isotope labeling, which allows for high-precision, high-speed analysis of glycans. The introduction of stable isotopes through metabolic, enzymatic, and chemical approaches covers a wide range of sample types, including purified glycans and clinical specimens.
MICROCHEMICAL JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Illa Tea, Arnaud De Luca, Anne-Marie Schiphorst, Mathilde Grand, Sophie Barille-Nion, Eric Mirallie, Delphine Drui, Michel Krempf, Regis Hankard, Guillaume Tcherkez
Summary: The natural abundance of heavy stable isotopes is important in human physiology research, as it can easily identify changes in metabolic fluxes. This suggests the potential for medical diagnosis and prognostic using isotopes at natural abundance.
Article
Chemistry, Applied
Junfu Ji, Xinyu Liu, Xiaosong Hu, Fang Chen, Christoph Bueschl, Rainer Schuhmacher, Andrew L. Waterhouse, Lingjun Ma
Summary: This study successfully identified quinone reaction products in wine using a stable-isotope labelling approach combined with high-resolution mass spectrometry. Different nucleophiles were found to react in white wines and red wines.
Article
Biology
Ethan J. Sanford, Marcus B. Smolka
Summary: Protein phosphorylation is a common signaling mechanism, but analyzing phosphorylation events often lacks complete coverage. To improve coverage of phosphorylation sites on individual proteins, specific enrichment methods are necessary.
Article
Chemistry, Analytical
Yanxin Li, Chong Ma, Jinmao You, Shijuan Zhang
Summary: The study prepared deuterated dansylhydrazine through a one-step simple reaction, applied it to stable isotope labeling of aldehydes, enhanced quantitation accuracy, and minimized matrix effect.
MICROCHEMICAL JOURNAL
(2022)
Review
Spectroscopy
Xiaobo Tian, Hjalmar P. Permentier, Rainer Bischoff
Summary: This article summarizes the advances in liquid chromatography and mass spectrometry in proteome quantification approaches, focusing on the principles, benefits, and limitations of chemical isotope labeling-based methods. It also discusses the potential and limitations of multiplex isotope labeling approaches for data-independent acquisition mode.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Chemistry, Analytical
Cassio Lima, Howbeer Muhamadali, Royston Goodacre
Summary: We report the use of a novel technology, optical photothermal infrared (O-PTIR) spectroscopy, to simultaneously obtain infrared and Raman spectra from the same location of the sample for studying bacterial metabolism. The obtained infrared data from bulk populations and single cells were compared to conventional Fourier transform infrared (FTIR) spectroscopy to evaluate reproducibility. Raman spectra were analyzed to evaluate the isotopic incorporation. The study showed full incorporation of heavy isotopes by bacteria and successful discrimination between different labeled bacteria using Raman spectra. The limitations of O-PTIR technology to acquire Raman data from single bacterial cells and spectral artifacts induced by thermal damage were also discussed.
Article
Engineering, Environmental
Yao Lu, Chao Wang, Xin-Yang Zhang, Zhi-Wei Wang, Zhi-Min Song, Ye Du, Qing Hu, Qian-Yuan Wu, Hong-Ying Hu
Summary: The study found that during ozonation in the presence of bromide and ammonia, the formation of nitrogenous byproducts may lead to increased toxicity. Using UPLC-HRMS and an isotope labeling strategy, four newly formed nitrogenous byproducts were detected. This highlights the importance of paying attention to nitrogenous byproducts during ozonation in the presence of bromide and ammonia.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Review
Chemistry, Analytical
Di Yu, Lina Zhou, Xinyu Liu, Guowang Xu
Summary: The introduction of stable isotope labeling (SIL) technology has become a routine tool for functional metabolomics studies and allows for a deeper understanding of dynamic metabolic regulation in organisms. Mass spectrometry (MS) techniques have shown great vitality in this field by utilizing the different mass spectrometric characteristics between endogenous metabolites and their isotope-labeling forms. Recent advances in MS-based stable isotope-resolved metabolomics (SIRM) methods have expanded the breadth and depth of SIRM research by improving sample pretreatment, MS analysis, and data analysis. This review describes the recent progress of SIRM methods, summarizes their applications in metabolite identification, accurate quantification, and metabolic flux analysis, and discusses current limitations and challenges.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Agriculture, Multidisciplinary
Binsong Han, Lina Zhang, Ying Ma, Yanmei Hou, Kui Xie, Jinjing Zhong, Peng Zhou
Summary: We analyzed bovine and goat milk-based infant formula using quantitative phosphoproteomics and identified 200 phosphoproteins and 276 phosphorylation sites in bovine milk, and 75 phosphoproteins and 156 phosphorylation sites in goat milk. Among them, 99 phosphorylation sites from 26 shared phosphoproteins were differentially expressed between bovine and goat milk-based formulas. The identified phosphoproteins not only provide nutrition to infants but also have anti-inflammatory, antipathogenic, and other biological functions.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)