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COLMARm 13C-1H HSQC, HSQC-TOCSY and TOCSY Query and Verification

Tutorial and user manual
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STEP 1: Time domain spectra processing
   

HSQC spectrum (required)






TOCSY spectrum (optional)






HSQC-TOCSY spectrum (optional)






Bruker fid data format information
  • You can find raw fid data in the experimental folder, such as your_exp_name/2, where 2 is EXP ID. The file is usually named fid or ser
  • The acquisition status file is usually called acqus (not acqu) in the same folder as the FID data file.
  • You can also drag and drop fid and/or acqus file, or their parent folder to the box above.

STEP 1: Spectra processing





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Instructions
  • (Notice: spectra files can be nmrPipe (.ft2), sparky (.ucsf), Topspin ASCII format (.txt)) or Mnova .csv format. The server uses the file extension to distinguish file formats!
  • The number of points per peak (PPP), which is given by the number of data points that sample the peak’s full width at half height (FWHH), is allowed to vary either from 6 to 20 (optimal: 12) points or from 4 to 12 (optimal: 8) points. This requirement can be fulfilled easily by applying proper fold of zero filling. Typically, 4 to 8 times ( -zf 2 or 3 in nmrPipe ) of zero-filling is required to reach these PPPs.
  • Please use the 2PI-Kaiser window function for apodization in the NMRPipe software with the command “SP -off 0.5 -end 0.896 -pow 3.684”. The resulting peak shapes can then be modeled in all dimensions with good accuracy using a Voigt profile that combines variable amounts of Lorentzian vs. Gaussian character.
  • When you adjust lowest contour level, peaks that are fall below it will become invisible. However, all peaks will be kept in the downloaded file.
STEP2: Peak picking and peak fitting
Choose peak picking method



Peak fitting is recommended only if compound quantification is planed. It may take up to several hours for a complex spectrum
Choose peak line shape in peak fitting


STEP3(optional): Spectral referencing
Choose solvent: water or chloroform.
Choose compounds as references:
DSS Alanine Leucine Glucose Lactic Acid

The server automatically the reference correction by matching the peaks patterns of selected known compounds against experimental peaks. In this process, match at least
out of known peaks.



1H: 13C:
STEP 4: Database query with spectral matching using chemical shift difference





B0 of experiment


Database selection:


Query algorithm:
data for database query and display.




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Drawing


Current contour level cutoff: 1
Current contour level cutoff: 1
Control: Brush an area to Zoom in, or remove peaks within this area. , ,

Peak list:




Visualization options:

  • Zoom scale:
  • plot size:
Show detail of one matched spin-system:
Data base peak Matched experimental peak Expected cross peaks
HSQC Lowest contour level: = 0
HSQC Negative lowest contour level: = 0

TOCSY Lowest contour level: = 0
Tocsy Negative lowest contour level: = 0

HSQC-TOCSY Lowest contour level: = 0
HSQC-TOCSY Negative lowest contour level: = 0


Save peak and compound information to local file
Using Space or Comma as delimiter.

List of compounds in our database

Reference

Questions or comments? Please feel free to contact us.

Acknowledgement

This web server and the research that led to it is supported by the National Institutes of Health (Grant R01 GM 066041).
Most chemical shifts in COLMAR database were retrieved from the existing databases listed below, which all allow public access.

*This information is only used for the compilation of our webserver usage data.

This server is last updated at October 18 2025 06:33:45.