References
Abadie, C., Lalande, J., Limami, A. M., & Tcherkez, G. (2021). Non‐targeted 13C metabolite analysis demonstrates broad re‐orchestration of leaf metabolism when gas exchange conditions vary. Plant, Cell & Environment, 44 (2), 445-457.
Allwood, J. W., De Vos, R. C. H., Moing, A., Deborde, C., Erban, A., Kopka, J., . . . Hall, R. D. (2011). Plant metabolomics and its potential for systems biology research: Background concepts, technology, and methodology. Methods in enzymology, 500 , 299-336.
Alzweiri, M., Khanfar, M., & Al-Hiari, Y. (2015). Variations in GC–MS Response Between Analytes and Deuterated Analogs. Chromatographia, 78 (3), 251-258.
Bowne, J. B., Erwin, T. A., Juttner, J., Schnurbusch, T., Langridge, P., Bacic, A., & Roessner, U. (2012). Drought Responses of Leaf Tissues from Wheat Cultivars of Differing Drought Tolerance at the Metabolite Level. Molecular Plant, 5 (2), 418-429.
Caban, M., & Stepnowski, P. (2020). The application of isotopically labeled analogues for the determination of small organic compounds by GC/MS with selected ion monitoring. Analytical Methods, 12 (30), 3854-3864.
Carroll, A. J., Badger, M. R., & Harvey Millar, A. (2010). The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets. BMC bioinformatics, 11 (1), 1-13.
Cui, J., Abadie, C., Carroll, A., Lamade, E., & Tcherkez, G. (2019). Responses to K deficiency and waterlogging interact via respiratory and nitrogen metabolism. Plant, Cell & Environment, 42 (2), 647-658.
Cui, J., Davanture, M., Lamade, E., Zivy, M., & Tcherkez, G. (2021). Plant low‐K responses are partly due to Ca prevalence and the low‐K biomarker putrescine does not protect from Ca side effects but acts as a metabolic regulator. Plant, Cell & Environment, 44 (5), 1565-1579.
Cui, J., Davanture, M., Zivy, M., Lamade, E., & Tcherkez, G. (2019). Metabolic responses to potassium availability and waterlogging reshape respiration and carbon use efficiency in oil palm. New Phytologist, 223 (1), 310-322.
De Vos, R. C. H., Moco, S., Lommen, A., Keurentjes, J. J. B., Bino, R. J., & Hall, R. D. (2007). Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nature protocols, 2 (4), 778-791.
Doerfler, H., Sun, X., Wang, L., Engelmeier, D., Lyon, D., & Weckwerth, W. (2014). mzGroupAnalyzer-predicting pathways and novel chemical structures from untargeted high-throughput metabolomics data. Plos One, 9 (5), e96188.
Domergue, J.-B., Lalande, J., Abadie, C., & Tcherkez, G. (2022). Compound-Specific 14N/15N Analysis of Amino Acid Trimethylsilylated Derivatives from Plant Seed Proteins.International Journal of Molecular Sciences, 23 (9), Article no. 4893.
Du, X., & Zeisel, S. H. (2013). Spectral deconvolution for gas chromatography mass spectrometry-based metabolomics: current status and future perspectives. Computational and structural biotechnology journal, 4 (5), e201301013.
Gaquerel, E., Kuhl, C., & Neumann, S. (2013). Computational annotation of plant metabolomics profiles via a novel network-assisted approach.Metabolomics, 9 (4), 904-918.
Garcia, A., & Barbas, C. (2011). Gas chromatography-mass spectrometry (GC-MS)-based metabolomics. In Metabolic Profiling (pp. 191-204): Springer.
Ghatak, A., Chaturvedi, P., & Weckwerth, W. (2018). Metabolomics in plant stress physiology. Plant Genetics and Molecular Biology , 187-236.
Högy, P., Keck, M., Niehaus, K., Franzaring, J., & Fangmeier, A. (2010). Effects of atmospheric CO2 enrichment on biomass, yield and low molecular weight metabolites in wheat grain.Journal of Cereal Science, 52 (2), 215-220.
Jansen, J. J., Allwood, J. W., Marsden-Edwards, E., van der Putten, W. H., Goodacre, R., & van Dam, N. M. (2009). Metabolomic analysis of the interaction between plants and herbivores. Metabolomics, 5 (1), 150-161.
Kaufmann, A., & Walker, S. (2017). Comparison of linear intrascan and interscan dynamic ranges of Orbitrap and ion‐mobility time‐of‐flight mass spectrometers. Rapid Communications in Mass Spectrometry, 31 (22), 1915-1926.
Kind, T., & Fiehn, O. (2006). Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm. BMC bioinformatics, 7 (1), 1-10.
Lu, H., Liang, Y., Dunn, W. B., Shen, H., & Kell, D. B. (2008). Comparative evaluation of software for deconvolution of metabolomics data based on GC-TOF-MS. TrAC Trends in Analytical Chemistry, 27 (3), 215-227.
Lu, W., Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., & Rabinowitz, J. D. (2017). Metabolite measurement: pitfalls to avoid and practices to follow. Annual Review of Biochemistry, 86 , 277.
Makarov, A. (2000). Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Analytical Chemistry, 72 (6), 1156-1162.
Makarov, A., Denisov, E., & Lange, O. (2009). Performance evaluation of a high-field Orbitrap mass analyzer. Journal of the American Society for Mass Spectrometry, 20 (8), 1391-1396.
Matsuda, F., Nakabayashi, R., Sawada, Y., Suzuki, M., Hirai, M. Y., Kanaya, S., & Saito, K. (2011). Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity. Frontiers in plant science, 2 , Article no. 40.
Matucha, M., Jockisch, W., Verner, P., & Anders, G. (1991). Isotope effect in gas—liquid chromatography of labelled compounds.Journal of Chromatography A, 588 (1), 251-258.
Misra, B. B. (2021). Advances in high resolution GC-MS technology: a focus on the application of GC-Orbitrap-MS in metabolomics and exposomics for FAIR practices. Analytical Methods, 13 (20), 2265-2282.
Misra, B. B., & Chen, S. (2015). Advances in understanding CO2 responsive plant metabolomes in the era of climate change. Metabolomics, 11 (6), 1478-1491.
Miyagawa, H., & Bamba, T. (2019). Comparison of sequential derivatization with concurrent methods for GC/MS-based metabolomics.Journal of bioscience and bioengineering, 127 (2), 160-168.
Molnár-Perl, I., & Katona, Z. F. (2000). GC-MS of amino acids as their trimethylsilyl/t-butyldimethylsilyl Derivatives: In model solutions III.Chromatographia, 51 (1), S228-S236.
Morrison, K. A., & Clowers, B. H. (2018). Contemporary glycomic approaches using ion mobility–mass spectrometry. Current Opinion in Chemical Biology, 42 , 119-129.
Mu, Y., Schulz, B. L., & Ferro, V. (2018). Applications of Ion Mobility-Mass Spectrometry in Carbohydrate Chemistry and Glycobiology.Molecules (Basel, Switzerland), 23 (10), Article no. 2557.
Nakabayashi, R., & Saito, K. (2015). Integrated metabolomics for abiotic stress responses in plants. Current opinion in plant biology, 24 , 10-16.
Nakabayashi, R., & Saito, K. (2017). Ultrahigh resolution metabolomics for S-containing metabolites. Current Opinion in Biotechnology, 43 , 8-16.
Perez de Souza, L., Alseekh, S., Naake, T., & Fernie, A. (2019). Mass Spectrometry-Based Untargeted Plant Metabolomics. Current Protocols in Plant Biology, 4 (4), e20100.
Peterson, A. C., McAlister, G. C., Quarmby, S. T., Griep-Raming, J., & Coon, J. J. (2010). Development and characterization of a GC-enabled QLT-Orbitrap for high-resolution and high-mass accuracy GC/MS.Analytical Chemistry, 82 (20), 8618-8628.
Phatarphekar, A., Buss, J. M., & Rokita, S. E. (2014). Iodotyrosine deiodinase: a unique flavoprotein present in organisms of diverse phyla.Molecular BioSystems, 10 (1), 86-92.
Przybylski, C., & Bonnet, V. (2021). Discrimination of isomeric trisaccharides and their relative quantification in honeys using trapped ion mobility spectrometry. Food Chemistry, 341 , Article no. 128182.
Qiu, F., Fine, D. D., Wherritt, D. J., Lei, Z., & Sumner, L. W. (2016). PlantMAT: A Metabolomics Tool for Predicting the Specialized Metabolic Potential of a System and for Large-Scale Metabolite Identifications.Analytical Chemistry, 88 (23), 11373-11383.
Ripszam, M., Grabic, R., & Haglund, P. (2013). Elimination of interferences caused by simultaneous use of deuterated and carbon-13 standards in GC-MS analysis of polycyclic aromatic hydrocarbons (PAHs) in extracts from passive sampling devices. Analytical Methods, 5 (12), 2925-2928.
Roessner, U., & Bowne, J. (2009). What is metabolomics all about?Biotechniques, 46 (5), 363-365.
Sanchez, D. H., Schwabe, F., Erban, A., Udvardi, M. K., & Kopka, J. (2012). Comparative metabolomics of drought acclimation in model and forage legumes. Plant, Cell & Environment, 35 (1), 136-149.
Shulaev, V., Cortes, D., Miller, G., & Mittler, R. (2008). Metabolomics for plant stress response. Physiologia plantarum, 132 (2), 199-208.
Taurog, A. (1999). Molecular evolution of thyroid peroxidase.Biochimie, 81 (5), 557-562.
Vinaixa, M., Schymanski, E. L., Neumann, S., Navarro, M., Salek, R. M., & Yanes, O. (2016). Mass spectral databases for LC/MS- and GC/MS-based metabolomics: State of the field and future prospects. TrAC Trends in Analytical Chemistry, 78 , 23-35.
Zarate, E., Boyle, V., Rupprecht, U., Green, S., Villas-Boas, S. G., Baker, P., & Pinu, F. R. (2016). Fully automated trimethylsilyl (TMS) derivatisation protocol for metabolite profiling by GC-MS.Metabolites, 7 (1), 1.
Zheng, J., Johnson, M., Mandal, R., & Wishart, D. S. (2021). A Comprehensive Targeted Metabolomics Assay for Crop Plant Sample Analysis. Metabolites, 11 (5), Article no. 303.
Table 1. Common analytes that share both similar nominal mass signals and retention time but can be distinguished using exact mass . For each example, the elemental composition of the fragment and its exact mass is shown. When the observed mass of interest belongs to the isotopic pattern, it is indicated with the isotope in front (13C). See also Fig. 4 for a detailed analysis of two examples, with fragment chemical structure. This table shows couple of analytes with a difference in retention time of less than 0.4 min. (*) Note that m/z ions at ≈226.092 Da can also come from a fragment of allantoin 2TMS (C4H18N4O3Si2, 226.09119 Da). All analytes and fragments in this table have been checked using authentic standards.