For baseline correction to work properly, make sure to leave, ideally, ~10% of blank regions on either side of the spectrum. Do not let peaks fall near the edges of the spectrum.

On the Varian system, two commands can be used to correct the baseline.

• dc
  • this command does a basic automatic zero order and 1st order baseline correction. Very effective at correcting overall baseline offset (zero order), but doesn't do much if at all, to baseline rolling and distortion.
  • does not require manual baseline points definition
    
  • cdc cancels the effect from dc
    
• bc
  • More powerful polynomial baseline correction, up to order 19.
  • requires baseline regions defined through integral reset points
  • bc(n) where n is from 1 to 20 apply (n-1)th order of polynomial correction. By default, n=1 uses a spline fit. Most often bc is sufficient. But you can also try bc(3) etc if more complicated curvature is present in the spectrum baseline.
  • bc('unbc') removes the previous baseline correction with bc. Do this before re-apply new baseline correction.

Procedure

Varian's automatic baseline picking and correction
Click the following panels or buttons: Process->Display->Autofind integrals. Green lines (in partial integral mode) covering the peak regions will be shown. Then, click Baseline Correct. This appears to work well most of the times.

Clear integrals after baseline correction by tying cz in command area or click the Delete All Integral Regions button on the right side. Continue to pick integral resets points if desired.

Manual baseline picking and correction
Use bc for full baseline correction if good spectral quality and integral accuracy is needed.

• Type wft f full to process/display full spectrum.
  
• Phase spectrum either with aph and/or manual correction if needed.
  
• Display full integral and define baseline regions using the same procedure as when picking integral reset points, except that the reset points should enclose larger areas of peaks (not too close to any peak base) and not to pick points inside clusters of peaks. The focus is to define the areas (baselines) that are NOT in the integral areas.
• Once finished, click the cursor/box button to exit the integral resets mode. The integral mode is now in Partial Integral. If not, type inmod='partial' or toggle through the integral display button into Partial Integral mode. The areas NOT covered by the solid green lines are the baseline regions that will be used for baseline correction. Make sure the areas not covered by any green lines do not have any peaks present.
• Type bc in the command area to apply the baseline correction.
• Once done, if you want to repick detailed integral points, type cz and start integral resets.
  

Example

Manual picking baseline areas

wft f full


Reset integral points. Note that you do not have to fine-pick peaks because the focus is to define the baseline areas (not covered by solid green lines).


Baseline correction with bc