Abstract
This paper gives a step-by-step account of how to install, set up, and run MetAlign software, which can be downloaded freely (http://www.metalign.wur.nl/UK/Download+and+publications). The software is used for accurate mass and nominal mass data coming from different kinds of GC-MS and LC-MS platforms. The algorithms are beyond the scope of this paper and were published separately.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Tolstikov, V.V., Lommen, A., Nakanishi, K., Tanaka, N., Fiehn, O. (2003) Monolithic Silica-Based Capillary Reversed-Phase Liquid Chromatography/Electrospray Mass Spectrometry for Plant Metabolomics. Anal. Chem., 75, 6737–6740.
Vorst, O., de Vos, C.H.R., Lommen, A., Staps, R.V., Visser, R.G.F., Bino, R.J., Hall, R.D. (2005) A non-directed approach to the differential analysis of multiple LC MS-derived metabolic profiles. Metabolomics 1, 169–180.
Tikunov, Y., Lommen, A., de Vos, C.H.R., Verhoeven, H.A., Bino, R.J., Hall, R.D., Lindhout, et al (2005) A Novel Approach for Non-targeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles. Plant Physiol. Break Through Technologies Section 139, 1125–1137.
America, A.H.P., Cordewener, J.H.G., Van Geffen, H.A., Lommen, A., Vissers, J.P.C., Bino, R.J., Hall, R.D. (2006) Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS. Proteomics, 6, 641–653.
Keurentjes, J.J.B., Jingyuan, F., de Vos, C.H.R., Lommen, A., Hall, R. D., Bino, R. J., van der Plas et al (2006) The genetics of plant metabolism. Nature Genetics (Technical Report) 38, 842–849.
Lommen, A., van der Weg, G., van Engelen, M. C., Bor, G., Hoogenboom, L.A.P., Nielen, M.W.F. (2007) An untargeted metabolomics approach to contaminant analysis: Pinpointing potential unknown compounds. Analytica Chimica Acta, 584, 43–49.
de Vos, C.H.R., 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, 778–791.
Ducruix, C., Vailhen, D., Werner, E., Fievet, J.B., Bourguignon, J., Tabet, J.-C., Ezan, E., et al (2008), Metabolomic investigation of the response of the model plant Arabidopsis thaliana to cadmium exposure: Evaluation of data pretreatment methods for further statistical analyses. Chemometrics and Intelligent Laboratory Systems, 91, 67–77.
Matsuda, F., Yonekura-Sakakibara, K., Niida, R., Kuromori, T., Shinozaki, K., Saito, K. (2009) MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. The Plant Journal, 57, 555–577.
Lommen, A. (2009) MetAlign: an interface-driven, versatile metabolomics tool for hyphenated full-scan MS data pre-processing. Anal. Chem., 81, 3079–3086.
See Masslynx manual: http://www.waters.com/.
See HP 5970 MSD manual: http://www.gmi-inc.com/Agilent-HP-5970-Mass-Spectrometer.html.
See Xcalibur manual: http://www.thermo.com.
Stein, S.E. (1999) An Integrated Method for Spectrum Extraction and Compound Identi-fication from GC/MS Data. J. Am. Soc. Mass Spectrom, 10, 770–781.
Acknowledgements
This work was supported by the Dutch Ministry of Agriculture, Nature and Food Quality, Strategic Research Funds RIKILT-WUR (project 77232903), Statutory Research Tasks (theme 3): veterinary drugs (project 87203001), The Netherlands Toxicogenomics Centre (NTC), contract AIR3-CT94-2311 (European Commission DG XII), and the EU-Framework VI programme : EU-METAPHOR (FP6: FOOD-CT-2006-036220), EU-NOFORISK (FP6: FOOD-CT2001-506387), EU-GMOCARE (QLK1-1999-00765). Datasets used in the development of MetAlign are from these projects and research consortia. Ric de Vos and Yury Tikunov of Plant Research International (Centre of Biosystems Genomics) are thanked for critical evaluation using their own data in the validation process of MetAlign.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Lommen, A. (2011). Data (Pre-)processing of Nominal and Accurate Mass LC-MS or GC-MS Data Using MetAlign. In: Hardy, N., Hall, R. (eds) Plant Metabolomics. Methods in Molecular Biology, vol 860. Humana Press. https://doi.org/10.1007/978-1-61779-594-7_15
Download citation
DOI: https://doi.org/10.1007/978-1-61779-594-7_15
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-593-0
Online ISBN: 978-1-61779-594-7
eBook Packages: Springer Protocols