Hi everyone! I am currently simulating hepatic lipid spectra in LCModel and have some questions regarding Section 11.7 of the manual.
Specifically, I am trying to fully understand the parameter AMP* (“effective number of protons”). The manual mentions that if the spectra in the file are scaled to yield mM, then would yield the concentration in mM of CH2 groups, and not necessarily of the whole molecules.AMP*.basisAMP = 2.0
Could someone explain a bit more in-depth how LCModel handles this parameter internally?
Any guidance would be greatly appreciated. Best regards!
Basically, the AMP parameter determines the area (amplitude) of a simulated basis function signal. This is in units of protons.
How does LCModel know what the area corresponding to one proton should be? It looks into the metabolite basis set that you have to provide - remember you have to provide one even if you’re just simulating lipids or MMs. Specifically, LCModel expects to find a singlet at a chemical shift of WSPPM in a basis function named WSMET stemming from N1HMET protons:
As you can see, by default it calculates the area of the 3.027 ppm Cr methyl singlet (which comes from 3 protons). The total area of this reference singlet is stored in the AREABA variable that is listed in the .print output file. From there, it knows how much the area of a single proton is (\frac{AREABA}{N1HMET}) and can simulate a Gaussian MM/lipid basis function with the area AMP*\frac{AREABA}{N1HMET}.
Obviously, these simulated signals do not correspond to actual MM or fatty acid molecules (which are composed of groups with varying chemical shifts, different relative amplitudes depending on chain length, different relaxation times, etc.) - that’s why the statement says you get estimates of ‘groups’ rather than molecules. Note that you’d also have to do an appropriate relaxation correction to arrive at anything even approximately resembling mM units. Terminology-wise, I would absolutely use the phrase ‘institutional units’ here.
