Abstract
The success of metabolomic analyses relies on the detection method used to analyze the samples and the management of the chemical data. To interrogate the information with biological hypotheses, scientists require a user friendly and manageable way of processing Big Data. Microbial Natural Products Drug Discovery is getting benefits from these techniques that can be applied for a detailed evaluation of the changes in the chemical diversity of the metabolites that a different treatment can induce in a given producer strain. Liquid Chromatography in tandem with Mass Spectrometry (LC-MS) is considered the best cost/effective technique to analyze biological samples that contain metabolites. Simplifying the complexity of these LC-MS sources in a user friendly way can help with the interrogation of the information for a correct use of statistics and scientific hypothesis testing. We describe herein MASS Studio 1.0, a new generation software utility that simplifies LC-MS traces to allow metabolomics analysis on large sets of microbial Natural Products samples in a Drug Discovery Project environment.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Garcia, J.B., Tormo, J.R.: HPLC studio: a novel software utility to perform HPLC chromatogram comparison for screening purposes. J. Biomol. Scr. 8, 305–315 (2003)
Tormo, J.R., et al.: A method for the selection of production media for actinomycete strains based on their metabolite HPLC profiles. J. Ind. Microbiol. Biotechnol. 30, 582–588 (2003)
Tormo, J.R., Garcia, J.B.: Automated analyses of HPLC profiles of microbial extracts - a new tool for drug discovery screening. In: Zhang, L., Demain, A.L. (eds.) Nature Product: Drug Discovery and Therapeutic Medicine, pp. 57–75. Humana Press Inc., Totowa (2005)
Gonzalez-Menendez, V., et al.: Differential induction of secondary metabolite profiles in endophyte fungi by the addition of epigenetic modifiers. Planta Med. 81, 924 (2015)
Perez-Victoria, I., Martin, J., Reyes, F.: Combined LC/UV/MS and NMR strategies for the dereplication of marine natural products. Planta Med. 82, 857–871 (2016)
Hur, M., Campbell, A.A., Almeida-de-Macedo, M., Li, L., Ransom, N., Jose, A., Wurtele, E.S.: A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Nat. Prod. Rep. 30, 565–583 (2013)
González-Menéndez, V., Pérez-Bonilla, M., Pérez-Victoria, I., Martín, J., Muñoz, F., Reyes, F., Tormo, J.R., Genilloud, O.: Multicomponent analysis of the differential induction of secondary metabolite profiles in fungal endophytes. Molecules 21, 234–250 (2016)
Ríos Peces, S., Díaz Navarro, C., Márquez López, C., Caba, O., Jiménez-Luna, C., Mel-guizo, C., Prados, J.C., Genilloud, O., Vicente Pérez, F., Pérez Del Palacio, J.: Untargeted LC-HRMS-based metabolomics for searching new biomarkers of pancreatic ductal adenocarcinoma: a pilot study. J. Biomol. Screen 21 (2016). doi:10.1177/1087057116671490
Ito, T., Odake, T., Katoh, H., Yamaguchi, Y., Aoki, M.: High-throughput profiling of microbial extracts. J. Nat. Prod. 74(5), 983–988 (2011)
Gonzalez-Menendez, V., Martin, J., Siles, J.A., Gonzalez-Tejero, R., Reyes, F., Platas, G., Tormo J.R., Genilloud, O.: Biodiversity and chemotaxonomy of Preussia isolates from the Iberian Peninsula. Two new species discovered. Mycol. Progress (2017, submitted)
Osada, H., Nogawa, T.: Systematic isolation of microbial metabolites for natural products depository (NPDepo). Pure Appl. Chem. 84(6), 1407–1420 (2012)
Lim, C.L., Nogawa, T., Uramoto, M., Okano, A., Hongo, Y., Nakamura, T., Koshino, H., Takahashi, S., Ibrahim, D., Osada, H.: RK-1355A and B, novel quinomycin derivatives isolated from a microbial metabolites fraction library based on NP-Plot screening. J. Antibiot. 67, 323–329 (2014)
Stadler, M.: Importance of secondary metabolites in the Xylariaceae as parameters for assessment of their taxonomy, phylogeny, and functional biodiversity. Curr. Res. Environ. Appl. Mycol. J. Fungal Biol. 1, 75–133 (2011)
Stadler, M., Læssøe, T., Fournier, J., Decock, C., Schmieschek, B., Tichy, H.-V., Peršoh, D.: A polyphasic taxonomy of Daldinia (Xylariaceae). Stud. Mycol. 77(1), 1–143 (2014)
Kim, W., Peever, T.L., Park, J.J., Park, C.M., Gang, D.R., Xian, M., Davidson, J.A., Infantino, A., Kaiser, W.J., Chen, W.: Use of metabolomics for the chemotaxonomy of legume-associated Ascochyta and allied genera. Sci. Rep. 6, 20192 (2016)
Acknowledgments
This work was carried out as part of the Master and PhD. Programs from the School of Master Degrees of the University of Granada.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Martínez, G., González-Menéndez, V., Martín, J., Reyes, F., Genilloud, O., Tormo, J.R. (2017). MASS Studio: A Novel Software Utility to Simplify LC-MS Analyses of Large Sets of Samples for Metabolomics. In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2017. Lecture Notes in Computer Science(), vol 10208. Springer, Cham. https://doi.org/10.1007/978-3-319-56148-6_20
Download citation
DOI: https://doi.org/10.1007/978-3-319-56148-6_20
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-56147-9
Online ISBN: 978-3-319-56148-6
eBook Packages: Computer ScienceComputer Science (R0)