Despite its young age, our company has already participated in numerous scientific collaborations. Indeed, more and more research institutes and universities decide to tap into metaSysX's resources and expertise as a comfortable and affordable option for expediting their research.

Below are several basic-research projects to which we contributed.



Mapping the Arabidopsis metabolic landscape by untargeted metabolomics at different environmental conditions


In this ambitious project, numerous novel genes that control secondary metabolism in the model plant Arabidopsis were identified by employing a so-called genome-wide association study: the abundance levels of thousands of metabolites from hundreds of Arabidopsis strains were mathematically correlated to known markers in the genome, establishing an information-rich network of gene–metabolite associations. LC–MS/MS fragment analysis, which often contributes to the annotation of ambiguous compounds, was performed at metaSysX.

Open publication


Lsd1 ablation triggers metabolic reprogramming of brown adipose tissue


Adipocytes are the lipid warehouses in animals. Whereas white adipocytes store fats and are responsible in great part for obesity, brown adipocytes dispense fat and provide energy. In this study, published in the high-impact Cell Reports, a gene encoding a demethylase was shown to be crucial in maintaining the characteristics of brown adipose tissue. Metabolomic and lipidomic profiling performed at metaSysX revealed a dramatic metabolic shift in brown adipocytes with a deactivated demethylase. Understanding the homeostasis of brown and white adipocates is crucial for addressing obesity.

Open publication


Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field


Crossing between different strains often results in offspring with improved qualities. In the case of crop plants this phenomenon, called heterosis or hybrid vigor, may translate to higher biomass, yield, or resistance to pathogens, and it has been extensively exploited by breeders. In this study metabolomic profiling, conducted at metaSysX, was performed on young seedling roots. The obtained data could be used to robustly predict heterosis. This constitutes a step in bridging the so-called greenhouse–field gap, a major challenge in breeding endeavors.

Open publication


Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4


The importance of stem cells for regenration of damaged tissue cannot be overstated. With time stem cells lose their capacity to differentiate, resulting in aging and death. Stress and disorders too may impair stem-cell function, again leading to accelarated aging. In this study an important epigenetic enzyme (Lsd1) was found to be a crucial regulator of the metabolic homeostasis of embryonic stem cells. Deleting this enzyme resulted in senescence in these stem cells and in severe metabolic imbalance—as determined by metabolomic profiling performed at metaSysX.

Open publication


Compound annotation in liquid chromatography/high-resolution mass spectrometry based metabolomics: robust adduct ion determination as a prerequisite to structure prediction in electrospray ionization mass spectra


In this method article scientists from Berlin present a new tool for the annotation of spectra deriving from electrospray ionization (ESI) mass spectrometry. Current approaches suffer from scant validation and are proprietry. The new tool is publically available and was, with metaSysX's help, validated against more than a thousand positive ESI spectra.

Open publication


A plant/fungal-type phosphoenolpyruvate carboxykinase located in the parasite mitochondrion ensures glucose-independent survival of Toxoplasma gondii

Open publication

A metabolic cooperativity of glucose and glutamine is essential for the lytic cycle of obligate intracellular parasite Toxoplasma gondii

Open publication

Toxoplasma gondii is a parasite that at any given time asymptomatically infects around half of the world's humans. In many cases disease can develop. In these two studies, conducted by Humboldt-University (Berlin, Germany) investigators, it is shown that when the parasite proliferates in the body it is dependent on glucose and glutamine as carbon sources. Metabolomic profiling of isotope-labeled parasites performed at metaSysX helped define carbon fluxes both in intact parasites and in ones deficient in certain transporters and enzymes that support central metabolism. The resemblence in metabolic phenotype between replicating Toxoplasma cells and cancer cells may hold therapeutic implications.



Medicinal bioprospecting of the Amazon rainforest: a modern Eldorado?


In this review article the potential of rainforest-derived natural products to be used as medicines is discussed, with a focus on the way new technologies can be utilized to tap into this resource. metaSysX scientists contributed their insights with regard to the usage of modern metabolomic analysis techniques in supporting combinatorial chemistry efforts to unravel new medicinal compounds from rainforest material.

Open publication


Metabolomics: Methode zur Authentizitätsprüfung am Beispiel von Wein


Metabolomics zur Authentizitätsprüfung


In this short review, published in the journal of the German Agricultural Society as well as in Das Deutsche Weinmagazin, one of metaSysX's mainstay collaborations is presented. The project revolved around the authentication of wine origin and quality. The profiling of thousands of samples resulted in a metabolomics-based mathematical model of impressive prediction capacity. This work underscores metaSysX's complementary competencies and diversity of activities.

Open publication


Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition


Like many other fruits, dates come in many shapes, forms, tastes, and consistencies. In this study, conducted in Qatar, metaSysX-assisted metabolomic and lipidomic profiling of many date varieties in various developmental stages helped to gain insight into the underlying mechanisms of natural variation in this fruit. The results show that dates start to metabolically diverge already when they are still unripe, leading eventually to distinct mature varieties.

Open publication

Check our team publications

Dates Metabolomics Reveals a Highly Dynamic Ripening Process Accounting for Major Variation in Fruit Composition
Diboun I., Mathew S., Al-Rayyashi M., Elrayess M., Torres M., Halama A. , Méret M., Mohney R., Karoly E., Malek J., Suhre K.
BMC Plant Biology 201515:291 DOI: 10.1186/s12870-015-0672-5

Discrimination of wine attributes by metabolome analysis.
Cuadros-Inostroza A, Giavalisco P, Hummel J, Eckardt A, Willmitzer L, Peña-Cortés H.
Anal Chem. 2010 May 1;82(9):3573-80. doi: 10.1021/ac902678t.

The transcription factor PHR1 regulates lipid remodeling and triacylglycerol accumulation in Arabidopsis thaliana during phosphorus starvation.
Pant BD, Burgos A, Pant P, Cuadros-Inostroza A, Willmitzer L, Scheible WR.
J Exp Bot. 2015 Apr;66(7):1907-18. doi: 10.1093

Linking gene expression and membrane lipid composition of Arabidopsis.
Szymanski J, Brotman Y, Willmitzer L, Cuadros-Inostroza A
Plant Cell. 2014 Mar;26(3):915-28. doi: 10.1105/tpc.113.118919. Epub 2014 Mar 18.

Trichoderma-plant root colonization: escaping early plant defense responses and activation of the antioxidant machinery for saline stress tolerance.
Brotman Y, Landau U, Cuadros-Inostroza A, Tohge T, Fernie AR, Chet I, Viterbo A, Willmitzer L.
PLoS Pathog. 2013 Mar;9(3):e1003221. doi: 10.1371/journal.ppat.1003221. Epub 2013 Mar 14. Erratum in: PLoS Pathog. 2013 Apr;9(4). doi:10.1371

Involvement of the hexose transporter gene LeHT1 and of sugars in resistance of tomato to tomato yellow leaf curl virus.
Sade D, Brotman Y, Eybishtz A, Cuadros-Inostroza A, Fernie AR, Willmitzer L, Czosnek H.
Mol Plant. 2013 Sep;6(5):1707-10. doi: 10.1093/mp/sst036. Epub 2013 Feb 21.

Lichen depsides and depsidones reduce symptoms of diseases caused by tobacco mosaic virus (TMV) in tobacco leaves.
Ramírez I, Araya S, Piovano M, Carvajal M, Cuadros-Inostroza A, Espinoza L, Garbarino JA, Peña-Cortés H.
Nat Prod Commun. 2012 May;7(5):603-6.

High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions.
Caldana C, Degenkolbe T, Cuadros-Inostroza A, Klie S, Sulpice R, Leisse A, Steinhauser D, Fernie AR, Willmitzer L, Hannah MA.
Plant J. 2011 Sep;67(5):869-84. doi: 10.1111/j.1365-313X.2011.04640.x. Epub 2011 Jul 11.

Metabolomic and transcriptomic stress response of Escherichia coli.
Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, Steinhauser D, Selbig J, Willmitzer L.
Mol Syst Biol. 2010 May 11;6:364. doi: 10.1038/msb.2010.18.

TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data.
Cuadros-Inostroza A, Caldana C, Redestig H, Kusano M, Lisec J, Peña-Cortés H, Willmitzer L, Hannah MA.
BMC Bioinformatics. 2009 Dec 16;10:428. doi: 10.1186/1471-2105-10-428.

High-resolution direct infusion-based mass spectrometry in combination with whole 13C metabolome isotope labeling allows unambiguous assignment of chemical sum formulas.
Giavalisco P, Hummel J, Lisec J, Cuadros-Inostroza A, Catchpole G, Willmitzer L.
Anal Chem. 2008 Dec 15;80(24):9417-25. doi: 10.1021/ac8014627.

Metabolic labeling and membrane fractionation for comparative proteomic analysis of Arabidopsis thaliana suspension cell cultures.
Szymanski WG, Kierszniowska S, Schulze WX.
J Vis Exp. 2013 Sep 28;(79):e50535. doi: 10.3791/50535.

Arabidopsis nanodomain-delimited ABA signaling pathway regulates the anion channel SLAH3.
Demir F, Horntrich C, Blachutzik JO, Scherzer S, Reinders Y, Kierszniowska S, Schulze WX, Harms GS, Hedrich R, Geiger D, Kreuzer I.
Proc Natl Acad Sci U S A. 2013 May 14;110(20):8296-301. doi: 10.1073/pnas.1211667110. Epub 2013 Apr 29.

The use of heavy nitrogen in quantitative proteomics experiments in plants.
Arsova B, Kierszniowska S, Schulze WX.
Trends Plant Sci. 2012 Feb;17(2):102-12. doi: 10.1016/j.tplants.2011.11.001. Epub 2011 Dec 9. Review.

PAMP (pathogen-associated molecular pattern)-induced changes in plasma membrane compartmentalization reveal novel components of plant immunity.
Keinath NF, Kierszniowska S, Lorek J, Bourdais G, Kessler SA, Shimosato-Asano H, Grossniklaus U, Schulze WX, Robatzek S, Panstruga R.
J Biol Chem. 2010 Dec 10;285(50):39140-9. doi: 10.1074/jbc.M110.160531. Epub 2010 Sep 15.

Ratio-dependent significance thresholds in reciprocal 15N-labeling experiments as a robust tool in detection of candidate proteins responding to biological treatment.
Kierszniowska S, Walther D, Schulze WX.
Proteomics. 2009 Apr;9(7):1916-24. doi: 10.1002/pmic.200800443.

Definition of Arabidopsis sterol-rich membrane microdomains by differential treatment with methyl-beta-cyclodextrin and quantitative proteomics.
Kierszniowska S, Seiwert B, Schulze WX.
Mol Cell Proteomics. 2009 Apr;8(4):612-23. doi: 10.1074/mcp.M800346-MCP200. Epub 2008 Nov 25.

Ruthenium–Arene Catalysts Bearing N-Heterocyclic Carbene Ligands for Olefin Cyclopropanation and Metathesis
Méret M, A. M. Maj, A. Demonceau, L. Delaude
Monatsh. Chem. 2015, 146, 1099–1105 (DOI: 10.1007/s00706-015-1492-x).

From System Biology to System Chemistry: Metabolomic Procedures Enable Insights into Complex Chemical Reaction Networks in Water
Méret M, D. Kopetzki, T. Degenkolbe, S. Kleessen, Z. Nikoloski, V. Tellstroem, A. Barsch, J. Kopka, M. Antonietti, L. Willmitzer
RCS Adv., 2014, 4, 16777–16781 (DOI: 10.1039/C3RA42384K)

Poly(ADP-Ribose)Polymerase Activity Controls Plant Growth by Promoting Leaf Cell Number
P. Schulz, K. Jansseune, T. Degenkolbe, Méret M, H. Claeys, A. Skirycz, M. Teige, L. Willmitzer, M. A. Hannah
PloS ONE, 2014, 9(2) (DOI: 10.1371/journal.pone.0090322)

The Maize Leaf Lipidome Shows Multilevel Genetic Control and High Predictive Value for Agronomic Traits
C. Riedelsheimer*, Y. Brotman*, Méret M*, A. E. Melchinger, L. Willmitzer
Scientific Reports, 2013, 3(2479) (DOI: 10.1038/srep02479)
* CO-FIRTS AUTHORS

Transcript and Metabolite Analysis of the Trichoderma-induced Systemic Resistance Response to Pseudomonas syringae in Arabidopsis thaliana
Y. Brotman, J. Lisec, Méret M, I. Chet, L. Willmitzer, A. Viterbo
Microbiology 2012, 158(Pt 1):139–146 (DOI: 10.1099/mic.0.052621-0)

Decomposition of N-Hydroxylated Compounds During Atmospheric Pressure Chemical Ionization
S. Eichenberger, Méret M, S. Bienz, L. Bigler J.
Mass. Spectrom. 2009, 45, 190–197 (DOI: 10.1002/jms.1703)

Efficient and Flexible Solid-Phase Synthesis of N-Hydroxypolyamine Derivatives
Méret M, S. Bienz
Eur. J. Org. Chem. 2008, 5518–5525 (DOI: 10.1002/ejoc.200800677)

Metabolomic Profiling of 13 Diatom Cultures and Their Adaptation to Nitrate-Limited Growth Conditions
M. A. Bromke; J. S. Sabir; F. A. Alfassi; O. A. Abuzinadah, N. A. Redwan, M. Z. Mutwakil; M. P. Ashworth, Méret M, R. K. Jansen, L. Willmitzer
PLoS One. 2013; 8(6): e67340. doi: 10.1371/journal.pone.0067340

Organization and Evolution of Brain Lipidome Revealed by Large-Scale Analysis of Human, Chimpanzee, Macaque, and Mouse Tissues
Bozek K., Wei Y., Yan Z., Liu X., Xiong J., Sugimoto M., Tomita M., Pääbo S., Sherwood CC., Hof PR., Ely JJ., Yan Li, Steinhauser D., Willmitzer L., Giavalisco P., Philipp Khaitovich
Neuron 02/2015; 85(4). DOI:10.1016/j.neuron.2015.01.003

Sulphate fertilization ameliorates long-term aluminum toxicity symptoms in perennial ryegrass (Lolium perenne) Wulff-Zottele C., Hesse H., Fisahn J., Bromke M., Vera-Villalobos H., Yan Li, Frenzel F., Giavalisco P., Ribera-Fonseca A., Zunino L., Caruso I., Stohmann E., de la Luz Mora M.
Plant Physiology and Biochemistry 07/2014; 83C:88-99.

Systemic Analysis of Inducible Target of Rapamycin Mutants Reveal a General Metabolic Switch Controlling Growth in Arabidopsis thaliana.
Caldana C., Yan Li, Leisse A., Zhang Y., Bartholomaeus L., Fernie AR., Willmitzer L., Giavalisco P.
The Plant Journal 11/2012; 73(6). DOI:10.1111/tpj.12080

Ultra Performance Liquid Chromatography and High Resolution Mass Spectrometry for the Analysis of Plant Lipids
Hummel J., Segu S., Yan Li, Irgang S., Jueppner J., Giavalisco P.
Frontiers in Plant Science 10/2011; 2:54. DOI:10.3389/fpls.2011.00054

Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high‐resolution mass spectrometry
Giavalisco P., Yan Li, Matthes A., Eckhardt A., Hubberten HM., Hesse H., Segu S., Hummel J., Köhl K., Willmitzer L.
The Plant Journal 07/2011; 68(2):364 - 376. DOI:10.1111/j.1365-313X.2011.04682.x