Hi there!
I have inversion data that I’m trying to quantify in LCModel. I’m using the CHSIMU parameter to create models for the macromolecules, and have included a basis set with my inverted metabolites. The fit is good, however, the water corrected values I’m getting are very low (e.g. 4E-4). I wondered if there was perhaps I setting I was missing? ATTH2O is set to 1 and WCONC is set to 55510.
Any thoughts would be appreciated.
Thanks!
Tiffany
Hi Tiffany!
Are all the concentration estimates low, or just those for the MM?
Any chance you could share a config file or sample output data (either here or by email)?
Without this I’m guessing a bit, but the first thing I’d want to check is whether the scaling reference metabolite (default Cr @ 3ppm, defined by WSMET, WSPPM, N1HMET) is meaningful and behaving as expected? Do you see any errors/warnings in the output? For inversion data, I wonder if AREABA 3 might be your problem (ref page 156 of the LCModel manual)
Otherwise, I’d be looking at is the input supplied to makebasis, checking that AUTOSC, CONC, CONCSD settings are appropriate.
Hope this helps a bit.
Alex.
Hi Alex,
Thanks for your reply. I thought the same and had originally changed WSMET to be one of the MMs (as the majority of the metabolites we model inverted) but it didn’t make a difference. However going back I changed it to PCr (the only one of our metabolites that isn’t inverted) and now the values look correct, so if anyone else has this issue and comes across this thread, it looks like you can’t use simulated MMs for LCModel scaling.
Tiffany
Yes, I believe that is because it would make the definition of the “one proton area” circular. The MMs & lipids are simulated internally (via the chsimu parameter), and their area is directly coupled to the area of the singlet defined in WSMET.
See LCModel manual Section 11.7 on the definition of chsimu:
amp* = the effective number of protons contributing to peak *. The amplitudes are scaled consistently with the spectra in the .BASIS file using WSMET, WSPPM & N1HMET as in Sec 10.2.2. So, if the spectra in the .BASIS file are scaled to yield mM, then AMP = 2.0 would yield mM of CH2 groups (not necessarily mM of molecules).