Hi!
In my data, I have slight difference in my chemical shifts. For example when 15N-HSQC spectrum is compared to NOESY-15N-HSQC spectrum. This might affect my Cyana calculations and Cyana might not pick up all the peaks it should pick up. For example, if in 15N-HSQC and NOESY-15N-HSQC pair the 15N shifts differ too much from each other, this could lead to situation where NOE peaks are not picked for certain diagonal peak (HN, N).
In Analysis, there is a Shift Differences window and in the window there is a Peak List Comparison tab (https://www.ccpn.ac.uk/documentation/analysis/popups/CalcShiftDifferencePopup.html). I have been using this Peak List Comparison and there is some inconsistency in the results. I am not sure why. I hope someone could give helpful answers?
So, is Peak List Comparison tab designed to be used with experiments that are same? Like two 15N-HSQC spectra? If I compare hCCcoNH to NOESY-13C-HSQC (Ca, Cb, Cg, etc.), will Peak List Comparison work? Or is this breaking it somehow and calculated ppm difference is not right?
One inconsistency, which I noticed, was that sometimes ppm difference in two Peak lists is not calculated for certain atom although both Peaks list have it. For example, tryptophan’s Hbb gets delta ppm, but Hba doesn’t. Why? Also, I am not sure what atom names I can use. For example, “Hb3” gives long list of results, but I am not sure what “Hb3” actually means.
Before I used Peak List Comparison, I tried to export peak list, export from resonances (using different Shift Lists) and so on. I would have calculated the ppm difference in Excel. Now I am wondering, if this is actually the best way to solve this. So, if someone have good advice how to efficiently compare NOE spectra’s shift differences to assignment spectra, I would like to hear it.
Regards,
Mikael
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