Product of dienst


RIKILT Wageningen UR, Plant Research International (PRI)

MetAlign is software voor het voorbewerken en vergelijken van data verkregen uit LC- en GC massaspectrometrie. MetAlign is ontwikkeld door RIKILT in nauwe samenwerking met Plant Research International. De rest van de informatie over MetAlign is in het Engels.

MetAlign is a software programme for the pre-processing and comparison of full scan nominal or accurate mass LC-MS and GC-MS data.

MetAlign was designed and written by Arjen Lommen of RIKILT Wageningen UR. Recently the algorithms behind MetAlign were published in Analytical Chemistry. It has been extensively tested in collaboration with Plant Research International.

MetAlignTM is a powerful computer software tool running under Windows (W7 64 bit, W7 32 bit, XP, NT, 2000) for the analysis, alignment and comparison of full-scan Mass Spectrometry datasets.

Recent publications

[1] V.V. Tolstikov, A. Lommen, K. Nakanishi, N. Tanaka, O. Fiehn, Anal. Chem. (2003) 75 6737-6740. Monolithic Silica-Based Capillary Reversed- Phase Liquid Chromatography/Electrospray Mass Spectrometry for Plant Metabolomics.
[2] O. Vorst, C.H.R. de Vos, A. Lommen, R.V. Staps, R.G.F. Visser, R.J. Bino, R.D. Hall,
Metabolomics 1 (2005) 169. A non-directed approach to the differential analysis of multiple LC MS-derived metabolic profiles
[3] Y. Tikunov, A. Lommen, C.H.R. de Vos, H.A. Verhoeven, R.J. Bino, R.D. Hall, P. Lindhout, A.G. Bovy, Plant Physiol. Break Through Technologies Section 139 (2005) 1125-1137. A Novel Approach for Non-targeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles.
[[4] A.H.P. America, J.H.G. Cordewener, H.A. Van Geffen, A. Lommen, J.P.C. Vissers, R.J. Bino, R.D. Hall, Proteomics 6 (2006) 641-653. Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS
[5] J.J.B. Keurentjes, F. Jingyuan, C.H.R. de Vos, A. Lommen, R. D. Hall, R. J. Bino, L. H. W. van der Plas, R. C. Jansen, D. Vreugdenhil, M. Koornneef, Nature Genetics (Technical Report) 38 (2006) 842-849. The genetics of plant metabolism.
[6] A. Lommen, G. van der Weg, M. C. van Engelen, G. Bor, L.A.P. Hoogenboom, M.W.F. Nielen, Analytica Chimica Acta 584 (2007) 43–49. An untargeted metabolomics approach to contaminant analysis: Pinpointing potential unknown compounds
[7] C.H.R. De Vos, S. Moco, A. Lommen, J.J.B. Keurentjes, R.J. Bino, R.D. Hall, Nature Protocols 2(4) (2007) 778. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry.
[8] A. Lommen, Anal. Chem. (2009) 2009 81(8):3079-86.  MetAlign: an interface-driven, versatile metabolomics tool for hyphenated full-scan MS data pre-processing.
[9] Berendsen BJ, Essers ML, Mulder PP, van Bruchem GD, Lommen A, van Overbeek WM, Stolker LA. J Chromatography A 1216(46):8177-86. Newly identified degradation products of ceftiofur and cephapirin impact the analytical approach for quantitative analysis of kidney.
[10] Jeroen C.W. Rijk, Arjen Lommen, Martien L. Essers, Maria J. Groot, Johan M. Van Hende, Timo G. Doeswijk and Michel W.F. Nielen,  Anal. Chem. (2009), 81 (16), pp 6879–6888.  Metabolomics Approach to Anabolic Steroid Urine Profiling of Bovines Treated with Prohormones.
[11] Arjen Lommen, Arjen Gerssen, J.Efraim Oosterink, Harrie J. Kools, Ainhoa Ruiz-Aracama Ruud J.B. Peters and Hans G.J. Mol. , Metabolomics (2011) 7:15–24 DOI 10.1007/s11306-010-0230-y. . Ultra-fast searching assists in evaluating sub-ppm mass accuracy enhancement in U-HPLC/Orbitrap MS data-y
[12] Ainhoa Ruiz-Aracama, Ad Peijnenburg, Jos Kleinjans, Danyel Jennen, Joost van Delft, Caroline Hellfrisch and Arjen Lommen. BMC Genomics (2011), 12:251-270 ( An untargeted multi-technique metabolomics approach to studying intracellular metabolites of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzop-dioxin

[13] de Bok, F. A., Janssen. P. W., Bayjanov, J. R., Sieuwerts, S., Lommen, A., van Hylckama Vlieg, J. E., & Molenaar, D. (2011) Volatile compound fingerprinting of mixed culture fermentations. Applied and Environmental Microbiology, 77(17):6233-9

[14] Arjen Lommen and Harrie Kools, Metabolomics (2012), 8: 719-726. MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware

[15] Jeroen C. W. Rijk, Ad A. C. M. Peijnenburg, Marco H. Blokland, Arjen Lommen, Ron L. A. P. Hoogenboom, and Toine F. H. Bovee, Chem. Res. Toxicol., 2012, 25 (8), pp 1720–1731. Screening for Modulatory Effects on Steroidogenesis Using the Human H295R Adrenocortical Cell Line: A Metabolomics Approach

[16] Arjen Lommen∗, Henk J. van der Kamp, Harrie J. Kools, Martijn K. van der Lee, Guido van der Weg, Hans G.J. Mol Journal of Chromatography A Volume 1263, 9 November 2012, Pages 169–178), metAlignID: A high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data.

[17] Arjen Lommen. Anal. Chem. (2014),  Just Accepted Manuscript, DOI: 10.1021/ac500667h   Ultra-fast PubChem searching combined with improved filtering rules for elemental composition analysis.

Citation indices of Arjen Lommen (contact person Metalign)

Related projects of others

Yury Tikunov (  MSClust is a software tool for analysis of GCMS and LCMS datasets derived from untargeted profiling followed by ion-wise chromatogram alignment. MSClust performs unsupervised clustering and extraction of putative metabolite mass spectra from ion-wise chromatographic alignment data.

Download of MSClust.

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