DynaMo MS-Analytics Facility

At the DynaMo Center three state-of-the-art LC-MS instruments are available: two high performance TripleQuadrupole Mass Spectrometers for targeted analysis of small metabolites and targeted proteomics and a Time-of-Flight Mass Spectrometer for untargeted metabolomics approaches. Our analytical facility enables us to analyze samples both with high sensitivity, accuracy and precision with a total sample throughput of ~ approx. 45000 sample injections per year. Thorough service and regular maintenance ensure high quality data. Since the first samples were run in early 2014 more than 42 scientific articles have been published with data that was generated on these instruments.

The instruments are available for researchers at the DynaMo Center, the Department for Plant and Environmental Sciences and for research collaborations with universities and also companies. Please contact us for further details.

Instrumentation

1. Agilent Ultivo TripleQuadrupole coupled to a 1290 Infinity II series UHPLC

Our new state-of-the-art TripleQuadrupole (QqQ) instrument allows for accurate quantification in a very large dynamic range (>6x106) with detection limits for many compounds in the sub-nmolar range. Multiple Reaction Monitoring (MRM) facilitates detection and quantification of a large numbers of different compounds within short LC runs (4-10 min) with high precision and accuracy. The Multisampler for up to 14 96-well or 384-well plates allows for high-throughput. In combination with the Multicoloumn compartment long unsupervised runs are even possible with different columns and solvents. This new instrument opens up for new possibilities in terms of sample throughput with highest accuracy and precision.

2. Bruker EVOQ-Elite TripleQuadrupole coupled to a Bruker Advance UHPLC

Our TripleQuadrupole (QqQ) work horse that has passed 225,000 sample injections (as of April 2020) over the last 6 years. Excellent instrument for many types of analysis that allows for accurate quantification in a large dynamic range with detection limits for many compounds in the low nmolar range. Multiple Reaction Monitoring (MRM) facilitates detection and quantification of a large numbers of different compounds within short LC runs (4-10 min) with high precision. We have developed a range of standard methods allowing for quantification of a variety of compounds (see list to the right for details). In addition we have established Selected Reaction Monitoring (SRM) methods for targeted proteomics in different organisms like E. coli, S. cerevisiae and Arabidopsis thaliana.

3. Bruker Compact micrOTOF-Q coupled to a Dionex Ultimate 3000RS UHPLC

Our Time-of-flight (TOF) instrument allows for determination of the accurate mass (< ±2 ppm) and facilitates identification of new compounds. The instrument is used for screening and metabolomics analysis of extracts mainly from plant and microbial sources. The TOF is coupled to a high performance UHPLC providing separation of analytes before they enter the mass spectrometer. The setup runs very robustly also over runs of more than 14 days or longer. More than 26000 data files have been generated since its installation in early 2014.

Publications

with data acquired on instruments of the DynaMo MS-Analytics Facility:

2022

Wang C, Poborsky M, Crocoll C, Nødvig CS, Mortensen UH, Halkier BA (2022) Comparison of Genome and Plasmid-based Engineering of Multi-gene Benzylglucosinolate Pathway in Saccharomyces cerevisiae. Applied and Environmental Microbiology bioRxiv: doi.org/10.1101/2020.07.08.193391 (in press).

Cowan M, Møller BL, Norton S, Knudsen C, Crocoll C, Furtado A, Henry R, Blomstedt C, Gleadow RM (2022) Cyanogenesis in the Sorghum Genus: From Genotype to Phenotype. MDPI Genes,13(1), 140. doi:10.3390/genes13010140

Giudice RD, Putkaradze N, Santos BM dos, Hansen CC, Crocoll C, Motawia MS, Fredslund F, Laursen T, Welner DH (2022) Structure guided engineering of key amino acids in UGT85B1 controlling substrate and stereo specificities in aromatic cyanogenic glucoside biosynthesis. the Plant Journal. doi:10.1111/tpj.15904

Hansted L, Crocoll C, Bitarafan Z, Andreasen C (2022) Clopyralid applied to winter oilseed rape (Brassica napus L.) contaminates the food products nectar, honey and pollen. Food Control, Volume 140, 2022, 109124. doi:10.1016/j.foodcont.2022.109124

Peña-Varas C, Kanstrup C, Vergara-Jaque A, González-Avendaño M, Crocoll C, Mirza O, Dreyer I, Nour-Eldin H, Ramírez D (2022) Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking. Int. J. Mol. Sci. 23(3), 1595. doi:10.3390/ijms23031595

2021

D'Amelia V, Docimo T, Crocoll C, Rigano MM (2021) Specialized Metabolites and Valuable Molecules in Crop and Medicinal Plants: The Evolution of Their Use and Strategies for Their Production. Genes, Jun 18;12(6):936. doi:10.3390/genes12060936

Hunziker P, Lambertz SK, Weber K, Crocoll C, Halkier BA, Schulz A (2021) Herbivore feeding preference corroborates optimal defense theory for specialized metabolites within plants. PNAS. 118 (47)  doi:10.1073/pnas.2111977118

Kazachkova Y, Zemach I, Panda S, Bocobza S, Vainer A, Rogachev I, Dong Y, Ben-Dor S, Veres D, Kanstrup C, Lambertz SK, Crocoll C, Hu Y, Shani E, Michaeli S, Nour-Eldin HH, Zamir D, Aharoni A (2021) The GORKY glycoalkaloid transporter is indispensable for preventing tomato bitterness. Nature Plants 7, 468–480. doi:10.1038/s41477-021-00865-6

Krause ST, Liao P, Crocoll C, Boachon B, Förster C, Leidecker F, Wiese N, Zhao D, Wood JC, Buell CR, Gershenzon J, Dudareva N, Degenhardt J (2021) The biosynthesis of thymol, carvacrol, and thymohydroquinone in Lamiaceae proceeds via cytochrome P450s and a short-chain dehydrogenase. Proceedings of the National Academy of Sciences, 118 (52). doi:10.1073/pnas.2110092118

Perby LK, Richter S, Weber K, Hieber AJ, Hess N, Crocoll C, Mogensen HK, Pribil M, Burow M, Nielsen TH (2021) Cytosolic phosphofructokinases are important for sugar homeostasis in leaves of Arabidopsis thaliana. Ann. Bot. doi:10.1093/aob/mcab122

Yang ZL, Nour-Eldin HH, Haenniger S, Reichelt M, Crocoll C, Seitz F, Vogel H, Beran F (2021). Sugar transporters enable a leaf beetle to accumulate plant defense compounds. Nature Communications. 12:2658.  doi:10.1038/s41467-021-22982-8

Wang C, Crocoll C, Agerbirk N, Halkier BA (2021) Engineering and optimization of the 2-phenylethylglucosinolate production in Nicotiana benthamiana by combining biosynthetic genes from Barbarea vulgaris and Arabidopsis thaliana. The Plant Journal. doi:10.1111/tpj.15212

2020

Montini, L., Crocoll, C., Gleadow, R., Motawia, M.S., Janfelt, C., Bjarnholt, N., 2020. Matrix-assisted laser desorption/ionization-mass spectrometry imaging of metabolites during sorghum germination. Plant Physiol. doi:10.1104/pp.19.01357

Katz, E., Bagchi, R., Jeschke, V., Rasmussen, A.R.M., Hopper, A., Burow, M., Estelle, M., Kliebenstein, D.J., 2020. Diverse allyl glucosinolate catabolites independently influence root growth and development. Plant Physiol. doi.org/10.1104/pp.20.0017

Thiesen, L., Belew, Z.M., Griem-Krey, N., Pedersen, S.F., Crocoll, C., Nour-Eldin, H.H., Wellendorph, P., 2020. The γ-hydroxybutyric acid (GHB) analogue NCS-382 is a substrate for both monocarboxylate transporters subtypes 1 and 4. Eur. J. Pharm. Sci. 143, 105203. doi.org/10.1016/j.ejps.2019.105203

Brey LF, Wlodarczyk AJ, Thøfner JFB, Burow M, Crocoll C, Nielsen I, Nielsen AJZ, Jensen PE (2020) Metabolic engineering of Synechocystis sp. PCC 6803 for the production of aromatic amino acids and derived phenylpropanoids. Metabolic Engineering. doi.org/10.1016/j.ymben.2019.11.002 

Hunziker P, Ghareeb H, Wagenknecht L, Crocoll C, Halkier BA, Lipka V, Schulz A, (2020). De novo indol-3-ylmethyl glucosinolate biosynthesis, and not long-distance transport, contributes to defence of Arabidopsis against powdery mildew. Plant Cell & Environment. doi.org/10.1111/pce.13766

Manzotti A, Bergna A, Burow M, Jørgensen HJL, Cernava T, Berg G, Collinge DB, Jensen B (2020) Insights into the community structure and lifestyle of the fungal root endophytes of tomato by combining amplicon sequencing and isolation approaches with phytohormone profiling. FEMS Microbiology Ecology. doi.org/10.1093/femsec/fiaa052

Wang C, Dissing MM, Agerbirk N, Crocoll C, Halkier BA (2020) Characterization of Arabidopsis CYP79C1 and CYP79C2 by Glucosinolate Pathway Engineering in Nicotiana benthamiana Shows Substrate Specificity Toward a Range of Aliphatic and Aromatic Amino Acids. Front Plant Sci. doi: 10.3389/fpls.2020.00057

2019

Aghajanzadeh TA, Prajapati DH, Burow M. Copper toxicity affects indolic glucosinolates and gene expression of key enzymes for their biosynthesis in Chinese cabbage. Archives of Agronomy and Soil Science. [in press] doi.org/10.1080/03650340.2019.1666208

Wulff N, Ernst HA, Jørgensen ME, Lambertz SK, Maierhofer T, Belew ZM, Crocoll C, Motawia MS, Geiger D, Jørgensen FS, Mirza O, Nour-Eldin HH (2019) An Optimized Screen Reduces the Number of GA Transporters and provides Insights into NPF Substrate Determinants. Frontiers in Plant Science. doi.org/10.1101/670174 

Rakpenthai A, Burow M, Olsen CE, Sirikantaramas S (2019) Metabolic Changes and Increased Levels of Bioactive Compounds in White Radish (Raphanus sativus) Sprouts Elicited by Oligochitosan. Agronomy. doi.org/10.3390/agronomy9080467

Mellor SB, Vinde MH, Nielsen AZ, Hanke GT, Abdiaziz K, Roessler MM, Burow M, Motawia MS, Møller BL, Jensen PE (2019) Defining optimal electron transfer partners for light-driven cytochrome P450 reactions. Metab Eng. doi.org/10.1016/j.ymben.2019.05.003

Xu D, Hunziker P, Koroleva O, Blennow A, Crocoll C, Schulz A, Nour-Eldin HH, Halkier BA (2019) GTR-mediated radial import directs accumulation of defensive glucosinolates to sulfur-rich cells (S-cells) in phloem cap of inflorescence stem of Arabidopsis thaliana. Mol Plant. 2019. doi.org/10.1016/j.molp.2019.06.008

Petersen A, Hansen LG, Mirza N, Crocoll C, Mirza OA, Halkier BA (2019) Changing substrate specificity and iteration of amino acid chain elongation in glucosinolate biosynthesis through targeted mutagenesis of Arabidopsis methylthioalkylmalate synthase 1. Biosci Rep.39(7) doi.org/10.1042/BSR20190446

Aghajanzadeh TA, Reich M,  Hawkesford MJ, Burow M (2019) Sulfur metabolism in Allium cepa is hardly affected by chloride and sulfate salinity. Archives of Agronomy and Soil Science. Vol. 65 No.7. doi.org/10.1080/03650340.2018.1540037

Martens HJ, Sørensen S, Burow M, Veierskov B (2019) Characterization of top leader elongation in Nordmann Fir (Abies nordmanniana). Journal of Plant Growth Regulation. doi.org/10.1007/s00344-019-09938-5

Petersen A, Crocoll C, Halkier BA (2019) De Novo production of benzyl glucosinolate in Escherichia coli. Metab Eng. doi.org/0.1016/j.ymben.2019.02.004

Ehlert M, Jagd LM, Braumann I, Dockter C, Crocoll C, Motawia MS, Møller BL, Lyngkjær MF (2019) Deletion of biosynthetic genes, specific SNP patterns and differences in transcript accumulation cause variation in hydroxynitrile glucoside content in barley cultivars. Sci Rep. 9(1) 5730. doi.org/0.1038/s41598-019-41884-w

Santamaría E, Martínez M, Arnaiz A, Rioja C, Burow M, Grbic V, Díaz I (2019) An Arabidopsis TIR-Lectin Two-Domain Protein Confers Defense Properties against Tetranychus urticae. Plant Physiol. 179: 1298–1314. doi:10.1104/pp.18.00951

2018

Nintemann S, Hunziker P, Andersen TG, Schulz A, Burow M, Halkier BA (2018) Localization of the glucosinolate biosynthetic enzymes reveals distinct spatial patterns for the biosynthesis of indole and aliphatic glucosinolates.  Physiologia Plantarum 163: 138-154. doi.org/10.1111/ppl.12672

Jæger D, Simpson BS, Ndi CP, Jäger AK, Crocoll C, Møller BL, Weinstein P, Semple SJ. (2018) Biological activity and LC-MS/MS profiling of extracts from the Australian medicinal plant Acacia ligulata (Fabaceae). Nat Prod Res 32: 576–581. doi.org/10.1080/14786419.2017.1318383.

Heskes AM, Sundram TCM, Boughton BA, Jensen NB, Hansen NL, Crocoll C, Cozzi F, Rasmussen S, Hamberger B, Hamberger B, Staerk D, Møller BL, Pateraki (2018)  Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus. Plant J.  93(5) 943-958. doi.org/10.1111/tpj.13822

Bjarnholt N, Neilson EHJ, Crocoll C, Jørgensen K, Motawia MS, Olsen CE, Dixon DP, Edwards R, Møller BL (2018). Glutathione transferases catalyze recycling of auto-toxic cyanogenic glucosides in sorghum. Plant J.  doi.org/10.1111/tpj.13923

2017

Malinovsky FG, Thomsen MF, Nintemann SJ, Jagd LM, Bourgine B, Burow M, Kliebenstein DJ (2017) An evolutionary young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway. eLife 6:e29353.

Vavitsas K, Rue EØ, Stefánsdóttir LK, Gnanasekaran T, Blennow A, Crocoll C, Gudmundsson S, Jensen PE (2017) Responses of Synechocystis sp. PCC 6803 to heterologous biosynthetic pathways. Microb Cell Fact. 16(1) 140

Nintemann SJ, Vik D, Svozil J, Bak M, Baerenfaller K, Burow M, Halkier BA (2017) Unravelling Protein-Protein Interaction Networks Linked to Aliphatic and Indole Glucosinolate Biosynthetic Pathways in Arabidopsis. Front Plant Sci 8

Jørgensen M, Crocoll C, Halkier B, Nour-Eldin HH (2017) Uptake assays in Xenopus laevis oocytes using liquid chromatography-mass spectrometry to detect transport activity. Bio-protocol 7:

Henriques de Jesus MPR, Zygadlo Nielsen A, Busck Mellor S, Matthes A, Burow M, Robinson C, Jensen PE (2017) Tat proteins as novel thylakoid membrane anchors organize a biosynthetic pathway in chloroplasts and increase product yield 5-fold. Metab Eng: 44 108-116.

Ionescu IA, López-Ortega G, Burow M, Bayo-Canha A, Junge A, Gericke O, Møller BL, Sánchez-Pérez R (2017) Transcriptome and Metabolite Changes during Hydrogen Cyanamide-Induced Floral Bud Break in Sweet Cherry. Front Plant Sci 8: 1233.

Jæger D, Simpson BS, Ndi CP, Jäger AK, Crocoll C, Møller BL, Weinstein P, Semple SJ (2017) Biological activity and LC-MS/MS profiling of extracts from the Australian medicinal plant Acacia ligulata (Fabaceae). Nat Prod Res 1–6.

Barba-Espín G, Glied S, Crocoll C, Dzhanfezova T, Joernsgaard B, Okkels F, Lütken H, Müller R (2017) Foliar-applied ethephon enhances the content of anthocyanin of black carrot roots (Daucus carota ssp. sativus var. atrorubens Alef.). BMC Plant Biol 17: 70.

Jørgensen ME, Xu D, Crocoll C, Ramírez D, Motawia MS, Olsen CE, Nour-Eldin HH, Halkier BA (2017) Origin and evolution of transporter substrate specificity within the NPF family. elife 6.

Payne RME, Xu D, Foureau E, Teto Carqueijeiro MIS, Oudin A, Bernonville TD de, Novak V, Burow M, Olsen C-E, Jones DM, Tatsis EC, Pendle A, Halkier BA, Geu-Flores F, Courdavault V, Nour-Eldin HH, O’Connor SE (2017) An NPF transporter exports a central monoterpene indole alkaloid intermediate from the vacuole. Nature Plants 3: 16208.

2016

Vik D, Crocoll C, Andersen TG, Burow M, Halkier BA (2016) CB5C affects the glucosinolate profile in Arabidopsis thaliana. Plant Signal Behav 11: e1160189.

Mellor SB, Nielsen AZ, Burow M, Motawia MS, Jakubauskas D, Møller BL, Jensen PE (2016)Fusion of ferredoxin and cytochrome P450 enables direct light-driven biosynthesis. ACS Chem Biol 11: 1862–1869.

Crocoll C, Halkier BA, Burow M (2016) Analysis and quantification of glucosinolates. In Stacey G, Birchler J, Ecker J, Martin CR, Stitt M, Zhou J-M (eds.), Current Protocols in Plant Biology pp 385–409. John Wiley & Sons, Inc., Hoboken, NJ, USA.

Francisco M, Joseph B, Caligagan H, Li B, Corwin JA, Lin C, Kerwin R, Burow M, Kliebenstein DJ (2016) The Defense Metabolite, Allyl Glucosinolate, Modulates Arabidopsis thaliana Biomass Dependent upon the Endogenous Glucosinolate Pathway. Front Plant Sci 7: 774.

Tal I, Zhang Y, Jørgensen ME, Pisanty O, Barbosa ICR, Zourelidou M, Regnault T, Crocoll C, Olsen CE, Weinstain R, Schwechheimer C, Halkier BA, Nour-Eldin HH, Estelle M, Shani E (2016) The Arabidopsis NPF3 protein is a GA transporter. Nat Commun 7: 11486.

Wlodarczyk A, Gnanasekaran T, Nielsen AZ, Zulu NN, Mellor SB, Luckner M, Thøfner JFB, Olsen CE, Mottawie MS, Burow M, et al. (2016) Metabolic engineering of light-driven cytochrome P450 dependent pathways into Synechocystis sp. PCC 6803. Metab Eng 33: 1–11.

Mirza N, Crocoll C, Erik Olsen C, Ann Halkier B (2016) Engineering of methionine chain elongation part of glucoraphanin pathway in E. coli. Metab Eng 35: 31–37.

Crocoll C, Mirza N, Reichelt M, Gershenzon J, Halkier BA (2016) Optimization of engineered production of the glucoraphanin precursor dihomomethionine in Nicotiana benthamiana. Frontiers in bioengineering and biotechnology 4: 14.

2015

Jensen LM, Kliebenstein DJ, Burow M (2015) Investigation of the multifunctional gene AOP3 expands the regulatory network fine-tuning glucosinolate production in Arabidopsis. Front Plant Sci 6: 762.

Jensen LM, Jepsen HSK, Halkier BA, Kliebenstein DJ, Burow M (2015) Natural variation in cross-talk between glucosinolates and onset of flowering in Arabidopsis. Front Plant Sci 6: 697.