NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics

Metabolomics

Volumn 13, Issue 4, 2017, Pages

  Jacob, D ^a   Deborde, C ^a   Lefebvre, M ^a   Maucourt, M ^a   Moing, A ^a  

^a UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

Graphical unit interface; NMR viewer; NMR based metabolomics; Spectra processing

Indexed keywords

CALIBRATION; EXPERIMENTAL DESIGN; HUMAN; METABOLOMICS; PROTON NUCLEAR MAGNETIC RESONANCE; SKILL; STATISTICAL ANALYSIS; ARTICLE; BIOLOGIST; METABOLIC FINGERPRINTING;

EID: 85013093641     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-017-1178-y     Document Type: Article

References (18)

1. Alonso, A., Marsa, S., & Julià, A. (2015). Analytical methods in untargeted metabolomics: State of the Art in 2015. Frontiers in Bioengineering and Biotechnology, 3, 23. doi:10.3389/fbioe.2015.00023.
2. Bloemberg, T. G., Gerretzen, J., Wouters, H. J. P., Gloerich, J., van Dael, M., Wessels, H. J. C. T., et al. (2010). Improved parametric time warping for proteomics. Chemometrics and Intelligent Laboratory Systems, 104(1), 65–74.
3. Bornet, A., Maucourt, M., Deborde, C., Jacob, D., Milani, J., Vuichoud, B., et al. (2016). Highly repeatable dissolution dynamic nuclear polarization for heteronuclear NMR metabolomics. Analytical Chemistry, 88(12), 6179–6183.
4. Candela, L., Castelli, D., & Pagano, P. (2013). Virtual research environments: An overview and a research agenda. Data Science Journal, 12, GRDI75–GRDI81.
5. Cloarec, O., Dumas, M., Craig, A., Barton, R., Trygg, J., Hudson, J., et al. (2005). Statistical total correlation spectroscopy: An exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. Analytical Chemistry, 77(5), 1282–1289.
6. Cruz, T., Balayssac, S., Gilard, V., Martino, R., Vincent, C., Pariente, et al. (2014). 1H NMR analysis of cerebrospinal fluid from Alzheimer’s disease patients: An example of a possible misinterpretation due to non-adjustment of pH. Metabolites, 4(1), 115–128. doi:10.3390/metabo4010115.
7. De Meyer, T., Sinnaeve, D., Gasse, B., Tsiporkova, E., Rietzschel, E., De Buyzere, M., et al. (2008). NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm. Analytical Chemistry, 80(10), 3783–3790.
8. Eddelbuettel, D., & Francois, R. (2011). Rcpp: Seamless R and C++ integration. Journal of Statistical Software, 40(8), 1–18.
9. Giacomoni, F., Le Corguillé, G., Monsoor, M., Landi, M., Pericard, P., Pétéra, M., et al. (2015). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics, 31, 1493–1495.
10. Larive, C., Barding, G. Jr., & Dinges, M. (2015). NMR spectroscopy for metabolomics and metabolic profiling. Analytical Chemistry, 205(87), 133–146.
11. Moing, A., Maucourt, M., Renaud, C., Gaudillere, M., Brouquisse, R., Lebouteiller, B., Gousset-Dupont, A., Vidal, J., Granot, D., Denoyes-Rothan, B., Lerceteau-Kohler, E., & Rolin, D. (2004). Quantitative metabolic profiling by 1-dimensional H-1-NMR analyses: Application to plant genetics and functional genomics. Functional Plant Biology, 31, 889–902.
12. R Core Team. (2014). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org/.
13. Ravanbakhsh, S., Liu, P., Bjorndahl, T. C., Mandal, R., Grant, J. R., Wilson, M., Eisner, R., Sinelnikov, I., Hu, X., Luchinat, C., Greiner, R., & Wishart, D. S. (2015). Accurate, fully-automated NMR spectral profiling for metabolomics. PLoS ONE, 10(5), e0124219.
14. Rocca-Serra, P., Salek, R. M., Arita, M., Correa, E., Dayalan, S., Gonzalez-Beltran, A., et al. (2016). Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics, 12, 14. doi:10.1007/s11306-015-0879-3.
15. Tredwell, G. D., Bundy, J. G., De Iorio, M., & Ebbels, T. M. D. (2016). Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine. Metabolomics, 12, 152. doi:10.1007/s11306-016-1101-y.
16. Vu, T. N., & Laukens, K. (2013). Getting your peaks in line: A review of alignment methods for NMR spectral data. Metabolites, 3(2), 259–276.
17. Xia, J., Sinelnikov, I. V., Han, B., & Wishart, D. S. (2015). MetaboAnalyst 3.0—making metabolomics more meaningful. Nucleic Acids Research, 43(W1), W251–W257.
18. Zheng, C., Zhang, S., Ragg, S., Raftery, D., & Vitek, O. (2011) Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection. Bioinformatics, 27(12):1637–1644. doi:10.1093/bioinformatics/btr118.