Technical Papers for Metabolomics

References from Emory’s Clinical Biomarkers Laboratory clinicalmetabolomics.org

Sample preparation and instrumental acquisition

• Johnson, J. M., T. Yu, F. H. Strobel and D. P. Jones (2010). “A practical approach to detect unique metabolic patterns for personalized medicine.” Analyst 135(11): 2864-2870.
• Soltow, Q., F. H. Strobel, K. G. Mansfield, L. Wachtman, Y. Park and D. P. Jones (2013). “High-performance metabolic profiling with dual chromatography-Fourier-transform mass spectrometry (DC-FTMS) for study of the exposome.”  Metabolomics. 
• Park, Y. H., K. Lee, Q. A. Soltow, F. H. Strobel, K. L. Brigham, R. E. Parker, . . . D. P. Jones (2012). “High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring.” Toxicology 295(1-3): 47-55. 

Data extraction and alignment

• Yu, T., Y. Park, J. M. Johnson and D. P. Jones (2009). “apLCMS–adaptive processing of high-resolution LC/MS data.” Bioinformatics 25(15): 1930-1936.
• Uppal, K., Q. A. Soltow, F. H. Strobel, W. S. Pittard, K. M. Gernert, T. Yu and D. P. Jones (2013). “xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.” BMC Bioinformatics 14: 15. 
• Yu, T., Y. Park, S. Li and D. P. Jones (2013). “Hybrid feature detection and information accumulation using high-resolution LC-MS metabolomics data.” J Proteome Res 12(3): 1419-1427.

Statistical analysis and pathway enrichment

• Li, S., Y. Park, S. Duraisingham, F. H. Strobel, N. Khan, Q. A. Soltow, . . . B. Pulendran (2013). “Predicting network activity from high throughput metabolomics.” PLoS Comput Biol 9(7): e1003123.
• Uppal, K., Q. A. Soltow, D. E. Promislow, L. M. Wachtman, A. A. Quyyumi, and D. P. Jones (2015). “MetabNet: An R Package for Metabolic Association Analysis of High-Resolution Metabolomics Data.” Front Bioeng Biotechnol 3(87).

Overall workflow

• Go, Y. M., K. Uppal, D. I. Walker, V. Tran, L. Dury, F. H. Strobel, . . . D. P. Jones (2014). “Mitochondrial metabolomics using high-resolution Fourier-transform mass spectrometry.” Methods Mol Biol 1198: 43-73.

Other external references

• Xia, J. and D.S. Wishart (2011). “Web-based inference of biological patterns, functions and pathways from metabolomics data using MetaboAnalyst.” Nat Protoc 6:743-60
• Sugimoto, M., Kawakami, M., Robert, M., Soga, T., and M. Tomita (2012). “Bioinformatics Tools for mass Spectroscopy-Based Metabolomic Data Processing and Analysis.” Curr Bioinform 7:96-108.