When I analyze NMR data for metabolomics combined with other omics, can I use relative quantification data but not absolute quantification to do multi-omics data analysis?
I will suggest the reading of the paper
Article Experimental design and quantitative analysis of microbial c...
Thank you, sir. Then Can I ask a question about NMR data analysis? For NMR, one compound have several peaks, then if I want to do quantification, should I combine all peaks and then calculate the concentration of that compound?
Hello,
Yes, you absolutely CAN. For multi-omics/ integrated-omics you hardly need anything in ABSOLUTE terms (neither are genomics, proteomics, transcriptomics!).
If you truly want to do NMR-based metabolomics (unsure when you say relative quantification in NMR?) then you MUST give a read and udnerstand this excellent recent paper: High‐Throughput Metabolomics by 1D NMR: https://onlinelibrary.wiley.com/doi/full/10.1002/anie.201804736 and follow all the original references they point to get the rationale of annotation and using such data for NMR metabolomics.
Also you may want to consult Dr. Ebbel's tools for NMR data quantification:
Thanks,
Biswa
P.S. Ignore comments above from others, which are non-specific.
esp. BATMAN i.e.,
Hao, J., Astle, W., De Iorio, M. and Ebbels, T.M., 2012. BATMAN—an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model. Bioinformatics, 28(15), pp.2088-2090.
and approaches such as:
Ebbels, T.M., Rodriguez-Martinez, A., Dumas, M.E. and Keun, H.C., 2018. Advances in Computational Analysis of Metabolomic NMR Data. NMR-based Metabolomics, 14, p.310.
Beckonert, O., Keun, H.C., Ebbels, T.M., Bundy, J., Holmes, E., Lindon, J.C. and Nicholson, J.K., 2007. Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nature protocols, 2(11), p.2692.
Weljie, A.M., Newton, J., Mercier, P., Carlson, E. and Slupsky, C.M., 2006. Targeted profiling: quantitative analysis of 1H NMR metabolomics data. Analytical chemistry, 78(13), pp.4430-4442.
Cavill, R., Kamburov, A., Ellis, J.K., Athersuch, T.J., Blagrove, M.S., Herwig, R., Ebbels, T.M. and Keun, H.C., 2011. Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PLoS computational biology, 7(3), p.e1001113.
Hope it helps.
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