Abstract
Mass spectrometry (MS) has become the analytical method of choice in plant metabolomics. Nevertheless, metabolite annotation remains a major challenge and implies the integration of structural searches in compound libraries with biological knowledge inferred from metabolite regulation studies. Here we propose a novel integrative approach to process and exploit the rich structural information contained in in-source fragmentation patterns of high-resolution LC–MS profiles. In this approach, a correlation matrix is first calculated from individual mass features extracted by xcms processing. Mass feature co-regulation patterns corresponding to metabolite in-source fragmentation are then detected and assembled into compound spectra using the R package CAMERA and processed for in silico fragment-based structure elucidation using MetFrag. We validate the performance of this approach for the rapid annotation of the twelve largest compound spectra, including four O-acyl sugars and six 17-hydroxygeranyllinalool diterpene glycosides in metabolic profiles of insect-attacked Nicotiana attenuata leaves. Additionally, we demonstrate the power of refining MetFrag metabolite annotations based on co-regulation patterns between known and unknown compounds in the correlation matrix and proposed structural annotations on two previously un-characterized O-acyl sugars. In summary, this novel approach facilitates compound annotation from in-source fragmentation patterns using correlation between intensities of mass features of one or several metabolites. Additionally, this analysis provides further support that insect herbivory activates major metabolic reconfigurations in N. attenuata leaves.
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References
Allen, E., Moing, A., Ebbels, T. M., Maucourt, M., Tomos, A. D., Rolin, D., et al. (2010). Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis. BMC Systems Biology, 4, 62.
Allwood, J. W., & Goodacre, R. (2010). An introduction to liquid chromatography-mass spectrometry instrumentation applied in plant metabolomic analyses. Phytochemical Analysis, 21, 33–47.
Breitling, R., Ritchie, S., Goodenowe, D., Stewart, M. L., & Barrett, M. P. (2006). Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data. Metabolomics, 2, 155–164.
Draper, J., Enot, D. P., Parker, D., Beckmann, M., Snowdon, S., Lin, W., et al. (2009). Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour ‘rules’. BMC Bioinformatics, 10, 227.
Dunn WB, Erban A, Weber RJM, Creek DJ, Brown M, Breitling R, Hankemeier T, Goodacre R, Neumann S, Kopka J, Viant MR (2012) Mass appeal: Metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics. in press doi:10.1007/s11306-012-0434-4.
Fukushima, A., Kusano, M., Redestig, H., Arita, M., & Saito, K. (2011). Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. BMC Systems Biology, 5, 1.
Gaquerel, E., Heiling, S., Schoettner, M., Zurek, G., & Baldwin, I. T. (2010). Development and validation of a liquid chromatography-electrospray ionization-time-of-flight mass spectrometry method for induced changes in Nicotiana attenuata leaves during simulated herbivory. Journal of Agriculture and Food Chemistry, 58, 9418–9427.
Gaquerel, E., Weinhold, A., & Baldwin, I. T. (2009). Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphigidae) and its natural host Nicotiana attenuata. VIII. An unbiased GCxGC-ToFMS analysis of the plant’s elicited volatile emissions. Plant Physiology, 149, 1408–1423.
Giri, A. P., Wunsche, H., Mitra, S., Zavala, J. A., Muck, A., Svatos, A., et al. (2006). Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. VII. Changes in the plant’s proteome. Plant Physiology, 142, 1621–1641.
Guha, R. (2007). Chemical informatics functionality in R. Journal of Statistical Software, 18(5), 1–16.
Halitschke, R., Gase, K., Hui, D., Schmidt, D. D., & Baldwin, I. T. (2003). Molecular interactions between the specialist herbivore Manduca sexta (lepidoptera, sphingidae) and its natural host Nicotiana attenuata. VI. Microarray analysis reveals that most herbivore-specific transcriptional changes are mediated by fatty acid-amino acid conjugates. Plant Physiology, 131, 1894–1902.
Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C. MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data Nucl Acid Res (in Press).
Heiling, S., Schuman, M. C., Schoettner, M., Mukerjee, P., Berger, B., Schneider, B., et al. (2010). Jasmonate and ppHsystemin regulate key Malonylation steps in the biosynthesis of 17-hydroxygeranyllinalool diterpene glycosides, an abundant and effective direct defense against herbivores in Nicotiana attenuata. Plant Cell, 22, 273–292.
Hill, D. W., Kertesz, T. M., Fontaine, D., Friedman, R., & Grant, D. F. (2008). Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra. Analytical Chemistry, 80, 5574–5582.
Hirai, M. Y., Klein, M., Fujikawa, Y., Yano, M., Goodenowe, D. B., Yamazaki, Y., et al. (2005). Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. Journal of Biological Chemistry, 280, 25590–25595.
Hirai, M. Y., Yano, M., Goodenowe, D. B., Kanaya, S., Kimura, T., Awazuhara, M., et al. (2004). Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proceedings of the National Academy of Sciences USA, 101, 10205–10210.
Jourdan, F., Breitling, R., Barrett, M. P., & Gilbert, D. (2008). MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics, 24, 143–145.
Keinanen, M., Oldham, N. J., & Baldwin, I. T. (2001). Rapid HPLC screening of jasmonate-induced increases in tobacco alkaloids, phenolics, and diterpene glycosides in Nicotiana attenuata. Journal of Agriculture and Food Chemistry, 49, 3553–3558.
Kim, S. G., Yon, F., Gaquerel, E., Gulati, J., & Baldwin, I. T. (2011). Tissue specific diurnal rhythms of metabolites and their regulation during herbivore attack in a native tobacco Nicotiana attenuata. PLoS One, 6, e26214.
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, 234.
Kuhl, C., Tautenhahn, R., Bottcher, C., Larson, T. R., & Neumann, S. (2012). CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84, 283–289.
Macel, M., Van Dam, N. M., & Keurentjes, J. J. (2010). Metabolomics: The chemistry between ecology and genetics. Molecular Ecology Resources, 10, 583–593.
Matsuda, F., Hirai, M. Y., Sasaki, E., Akiyama, K., Yonekura-Sakakibara, K., Provart, N. J., et al. (2010). AtMetExpress development: A phytochemical atlas of Arabidopsis development. Plant Physiology, 152, 566–578.
Neumann, S., & Bocker, S. (2010). Computational mass spectrometry for metabolomics: Identification of metabolites and small molecules. Analytical and Bioanalytical Chemistry, 398, 2779–2788.
Onkokesung, N., Gaquerel, E., Kotkar, H., Kaur, H., Baldwin, I. T., & Galis, I. (2012). MYB8 controls inducible phenolamide levels by activating three novel hydroxycinnamoyl-coenzyme A: Polyamine transferases in Nicotiana attenuata. Plant Physiology, 158, 389–407.
Rasche, F., Scheubert, K., Hufsky, F., Zichner, T., Kai, M., Svatos, A., et al. (2012). Identifying the unknowns by aligning fragmentation trees. Analytical Chemistry, 84, 3417–3426.
Rasche, F., Svatos, A., Maddula, R. K., Böttcher, C., & Böcker, S. (2011). Computing fragmentation trees from tandem mass spectrometry data. Analytical Chemistry, 83, 1243–1251.
Sansone, S. A., Fan, T., Goodacre, R., Griffin, J. L., Hardy, N. W., Kaddurah-Daouk, R., et al. (2007). The metabolomics standards initiative. Nature Biotechnology, 25, 846–848.
Sansone, S. A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., et al. (2012). Toward interoperable bioscience data. Nature Genetics, 44, 121–126.
Schymanski, E. L., Gallampois, C. M., Krauss, M., Meringer, M., Neumann, S., Schulze, T., et al. (2012). Consensus structure elucidation combining GC/EI-MS, structure generation, and calculated properties. Analytical Chemistry, 84, 3287–3295.
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., et al. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498–2504.
Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R., & Siuzdak, G. (2006). XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Analytical Chemistry, 78, 779–787.
Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., & Willighagen, E. (2003). The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. Journal of Chemical Information and Computer Sciences, 43, 493–500.
Steppuhn, A., & Baldwin, I. T. (2007). Resistance management in a native plant: nicotine prevents herbivores from compensating for plant protease inhibitors. Ecology Letters, 10, 499–511.
Steppuhn, A., Gase, K., Krock, B., Halitschke, R., & Baldwin, I. T. (2004). Nicotine’s defensive function in nature. PLoS Biology, 2, E217.
Szymanski, J., Jozefczuk, S., Nikoloski, Z., Selbig, J., Nikiforova, V., Catchpole, G., et al. (2009). Stability of metabolic correlations under changing environmental conditions in Escherichia coli–a systems approach. PLoS ONE, 4, e7441.
Weinhold, A., & Baldwin, I. T. (2011). Trichome-derived O-acyl sugars are a first meal for caterpillars that tags them for predation. Proceedings of the National Academy of Sciences USA, 108, 7855–7859.
Wolf, S., Schmidt, S., Muller-Hannemann, M., & Neumann, S. (2010). In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics, 11, 148.
Acknowledgments
We thank Prof. Ian T. Baldwin and Prof. Dierk Scheel for critical comments on the manuscript, Dr. Matthias Schöttner for analytical advices and for the measurement of metabolomic profiles, Sven Heiling for sharing his expertise on HGL-diterpene glycoside metabolism and Alexander Weinhold for help with the interpretation of AS.
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Gaquerel, E., Kuhl, C. & Neumann, S. Computational annotation of plant metabolomics profiles via a novel network-assisted approach. Metabolomics 9, 904–918 (2013). https://doi.org/10.1007/s11306-013-0504-2
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DOI: https://doi.org/10.1007/s11306-013-0504-2