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.