I use TopSpin for the processing of NMR spectra (phasing, peak picking and integration) but I want to process the obtained data further in R. For this, I specifically want to get the signal integration values (= peak areas) from TopSpin into R. I managed to export the spectral data as a JCAMP file (.dx) from TopSpin and to load this file in R, using the ReadJDX pacakage (https://cran.r-project.org/web/packages/readJDX/index.html) but I can't find the integration info within the JCAMP file. Does anybody know how to do this? Any other workflow for performing quantitative (1H-)NMR in R is also welcome!
Dear Thomas,
This is easy!
You perform your integration (e.g. manually done with the command .int or abs in automation).
After this you will in the dataset you worked on (speciefied by, disc, user, name, expno, procno - typically in a path like this /disc/user/nmr/name/expno/pdata/procno) a file integrals.txt which looks like this
Current data set:
NAME = 2024000002353 EXPNO = 710 PROCNO = 1
DU = /neo600x/data/serv/nmr
Number Integrated Region Integral
1 5.034 4.518 0.39267
2 4.339 3.749 0.43321
3 3.749 3.493 0.00443
4 2.134 1.584 0.13008
5 1.583 1.438 0.00394
6 1.438 1.155 0.03568
Here the last column is all integrals with the sum normalized 1.0
If you need the absolute values of integrals (e.g. for qNMR with external standard) it is a bit more tricky, because during the integration some renormalization is done. To get rid of this I wrote a little C-automation called NC_proc_to_intscl in my case.
int ncproc;
float intscl;
GETCURDATA
FETCHPARS("NC_proc", &ncproc);
intscl=pow(2,ncproc);
STOREPARS("INTSCL",intscl);
STOREPAR("CURPRIN","integrals.txt");
LI;
QUIT
You start this in Topspin with xau NC_proc_to_intscl.
After this the file will look like this
Current data set:
NAME = 2024000002353 EXPNO = 710 PROCNO = 1
DATPATH = /neo600x/data/serv/nmr
Number Integrated Region Integral
1 5.034 4.518 1.61146e+12
2 4.339 3.749 1.77784e+12
3 3.749 3.493 1.8161e+10
4 2.134 1.584 5.33821e+11
5 1.583 1.438 1.6173e+10
6 1.438 1.155 1.46442e+11
Now you have the absolute value integrals (linear in number of scans, and reciever gain, datapoints of spectrum and molar concentration of the compound*number of Nuclei inducing the signal).
I hope this is of help - good luck
Alfred
P.S. The integrals.txt file is by use of tojdx export also part of the *.dx file - look for the line
##BRUKER_FILE PROC=integrals.txt
The integral file is found below this line.
Thank you very much, Alfred Ross ! This is exactly what I was looking for.
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