Is there any feature which can help me with the indirect referencing for my 15N data? I tried to use the calibration from peaks but I am not confident to choose which peak that might not be massively perturbed. I tried with different location of the peak and it gave me slightly different CSP data.
Regards
Are you then looking for a global alignment routine?
Yes, sort of.
Hi Ireno,
If you are trying to look at CSPs, then really all the spectra should have been recorded with the same frequencies/offsets. The spectra should then all be referenced in the same way and not be moved relative to one another. If your 15N referencing is way off for some reason or other you can change this in the Spectrum Properties Dimensions tab (change the Referencing (ppm) value). But make sure this value is the same for all spectra.
The calibration from peaks is more for the situation where you are using spectra that were recorded on different spectrometers, for example, and you need to make sure that there is some internal consistency between the spectra. But to my mind, for looking at CSPs you precisely don’t want this.
Hope that helps,
Vicky
Dear Vicky,
My problem is that the referencing (ppm) value were completely different for two spectrum. My first spectrum ( wild type) shows 1H 8.789 and 15N 116.625. Second spectrum shows 1H 14.721 and 15N 134.146. When I changed the value of 2nd to the 1st, the overlaid far away.
Hi Ireno,
Referencing ppms apply at a particular point in the spectrum, so setting the same reference ppm isn’t necessarily logical unless you set the corresponding reference point.
Looking at your values (and knowing a little history of your project) I would guess that your original spectrum comes from your imported V2 project and has the reference point for each dimension set in the middle of the loaded data matrix (116 ppm ~ middle of 15N SW and 8.8 ppm ~ middle of the NH region (data to the right of the water probably discarded in processing)). analysis V2 tries to put the referencing point in the middle of the spectrum even when reading Bruker processed data.
Your new spectrum looks as if it has Bruker style referencing (processed in Topspin?) where the reference ppm applies at the point at the downfield end of each dimension. V3 doesn’t try to do anything with the reference information coming from the upstream processing software, it just leaves it as it is.
If the referencing for each spectrum was done correctly before loading into the CCPN software, you should not need to change it for either spectrum. If not, ideally you should go a step back and work out your referencing as best you can taking into account pH, salt & temperature or using your internal reference if you had one. If on the other hand, you’re confident that the conditions were the same for both, the sweep widths & offsets matched and they both have the same number of points in each of the dimensions, you should be able to just set the same reference ppm and point in each dimension to overlay them correctly. Choose the wild type or mutant values depending on which you trust the most!
Thanks Brian and Vicky for the help!