I’ll try to give some background to answer your question, but you might be better off just skipping to the references at the end, finding them and giving them a good read.
To calculate metabolite concentrations from signal amplitudes, you need to consider a few things.
First approximation is that the size of the signal is determined by the amount of the substance present - so more of metabolite X, gives a bigger signal for metabolite X.
Caveats, or adjustments to this approximation are that
- signal is also determined by the number of nuclei present in metabolite X, such that if metabolite X has 3 x as many nuclei of interest in its molecualr structure, it will give 3 times as much signal. (this is really just an extension of the more of somehting there is, the more signal you get rule, but at the level of the nuclei of interest, 1h, 31P etc.). Some metabolites will give rise to more than one peak, and you will need to know how many nuclei are giving rise to the peak you are fitting.
- relaxation properties also affect signal (T1 and T2 relaxation)
- spectral pattern, and the effects of J-coupling, can also impact the size of peak amplitudes - this is something to especially consider when using AMARES which just gives you amplitude, or area under the peak for the peaks you chose. As mentioned above some metabolites have more than one peak in their spectral pattern, and you will need to know how many nuclei are giving rise to the peak you are fitting, and if there are any other factors that could affect it.
- Any specific effects of the pulse sequence you are using (e.g. - are you using and editing pulse sequence - then editing efficency should be considered) - this is not likely to be an issue for MRS in the muscle.
Usually, factors 1 and 2 above are what most people consider when using AMARES for fitting, and is likely a good first approximation for work in the muscle.
So, more amplitude for X means more of X present - but how much? To get to this you need a reference signal of some sort, where the signal height:concentration ratio is known (or assumed). Usually this is acheived by using the signal of some metabolite wihtin the acquired spectrum, which has an known/assumed concentration. In brain MRS, this is usually unsuppressed water collected either just before, or just after the metabolite signals are also collected, although people may also use the total creatine peak (and just express the result as the ratio to creatine).
From the first aproximation:
[Met] = [Ref]X(SigMet/SigRef)
adding in the adjustments above
[Met] = [Ref]X((SigMet/#NucMet)/(SigRef/#NucRef))X(Relaxation correction factors)*
So, basiclally if you have a reference signal of known concentration, you can now work out your metabolite concentrations.
The problem you will have with your data is deciding if you actually do have a reference of known conentration in the spectra. Are you doing proton, or phopshorous (or other X nuclei) MRS? If phosphorous, ATP is usually used, with an assumed concentration of 8.2 mM. If Proton - I’m not sure what reference you want to use, but I use an unsupressed water scan.
*I’m not very good at using the forum tools to express these equations fully, so the above are somewhat abbreviated, for a good reference with more detail on brain MRS see:
Near, J., Harris, A. D., Juchem, C., Kreis, R., Marjańska, M., Öz, G., Slotboom, J., Wilson, M., & Gasparovic, C. (2020). Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: Experts’ consensus recommendations. NMR in Biomedicine, n/a(n/a), e4257. https://doi.org/10.1002/nbm.4257
and for 31P MRS in Muscle see:
Meyerspeer, M., Boesch, C., Cameron, D., Dezortova, M., Forbes, S. C., Heerschap, A., Jeneson, J. A. L., Kan, H. E., Kent, J., Layec, G., Prompers, J. J., Reyngoudt, H., Sleigh, A., Valkovic, L., Kemp, G. J., & Experts’ Working Group on, P. M. R. S. of S. M. (2020). 31P magnetic resonance spectroscopy in skeletal muscle: Experts’ consensus recommendations. NMR Biomed, e4246. https://doi.org/10.1002/nbm.4246
Hopefully this is helpful, and not too confusing. (and don’t get too worried if it is confusing right now - it’s not you, it’s just a little complicated).