I am trying to compare peak heights between several HSQC spectra as a measure of broadening for poorly resolved peaks. The peak heights calculated make sense within each spectra, but don’t when comparing spectra. I compared a few peaks manually by looking at 1D slices of the spectra in topspin. Comparing the peak heights extracted from CCPNMR do not match the differences I saw in the 1D slices.
How are peak heights calculated in CCPNMR? What parameters affect the calculated peak heights?
Can you share some screenshots? Have you checked the scaling values.
Also how did you check the slices in Ccpn ? did you use traces?
Have you tried to run the macro ‘extractSliceAtPeakPosition’ from a selected peak?
The 1D spectra below is comparing slices taken with the macro in CCPNMR (extractSliceAtPeakPosition).
The image below is from topspin comparing the slice from the same peak (the color scheme is the same). The intensity of the peak height of the red and green spectra are different in topspin vs. CCPNMR. The intensity of the red and green spectra are lower in CCPNMR. How do you check the scaling values in CCPNMR?
Hi,
it’s worth noting that Topspin uses a scaling parameter called NCPROC. When we import Bruker spectra we automatically scale all the spectra with the ncproc factor.
It might be worth checking whether the ncproc parameter is the same for all three spectra. When comparing intensities for Bruker spectra it is generally best to try and process all spectra with the same value for ncproc. Though in CcpNmr Analysis this should no longer be relevant as we now adjust the scaling automatically.
Vicky
I think that nc_proc is a bit of a red herring here (especially since we fully handle it now in V3 as well as V2).
The two slices you show are not actually the same slice through the spectra unless perhaps you have processed the data differently in one rather than the other (CcpNmr slice has more negative excursion next to the blue peak) and the relative intensities of the three peaks are quite similar in both.
I think we need to know a little more about your experiments to be able to help. Which of the three spectra are you comparing? Are the spectra acquired and processed with the same parameters (number of scans, increments, receiver gain, etc. ; window functions, zerofilling, etc.)? Are there some examples of peaks whose properties don’t change between your two conditions/samples (as well as ones that do)?
Best wishes
Brian
