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

General overview video of COLMAR suite of web servers

STEP 1: Time domain spectra processing
Your name and institute*: User chosen experimental name (optional):

HSQC spectrum (required)

HSQC fid file (required, usually called fid or ser):
acqus file (required, usually called acqus):
acqus2 file (required, usually called acqu2s):
pseudo-3D acquisition sequence
Negative imaginary data (indirect dimension)?

TOCSY spectrum (optional)

TOCSY fid file (required, usually called fid or ser):

acqus file (required, usually called acqus):

acqus2 file (required, usually called acqu2s):

HSQC-TOCSY spectrum (optional)

HSQC-TOCSY fid file (required, usually called fid or ser):

acqus file (required, usually called acqus):

acqus2 file (required, usually called acqu2s):

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.

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!

STEP2: Peak picking and peak fitting

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

STEP 4: Database query with spectral matching using chemical shift difference chemical shift cutoff (ppm) ¹H:
chemical shift cutoff (ppm) ¹³C:
Methylene relative chemical shift cutoff (ppm):
J splitting pattern chemical shift cutoff (ppm)
Matching ratio cutoff:
# of acquisition data points:

B0 of experiment 850 MHz
600 MHz
Other

Database selection: Hydrophilic metabolite database in water solvent
Hydrophobic and lipids metabolite database in organic chloroform solvent
Custom database

Query algorithm: Method 1 (match peak position only)
Method 2 (Match J-splitting patterns and peak positions, hydrophilic database only)

data for database query and display.

Noise level Drawing
Lowest contour level Logarithmic scale
Lowest contour level Logarithmic scale
Current contour level cutoff: 1
Current contour level cutoff: 1
Control: Brush an area to Zoom in, or remove peaks within this area. , ,
Good Fair Poor Not sure

Peak list:

Visualization options:

Zoom scale:
plot size:

Show detail of one matched spin-system:

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

Additional reference correction for TOCSY: ¹H:
Additional reference correction for HSQC-TOCSY: ¹H: ¹³C:

Download section

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

Good Fair

List of compounds in our database

Reference

Bingol, K.; Li, DW.; Zhang, B.; Brüschweiler, R.; Comprehensive metabolite identification strategy using multiple two-dimensional NMR spectra of a complex mixture implemented in the COLMARm web server; Anal. Chem; 2016, 88, 12411-12418;

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.

HMDB

BMRB

NMRShiftDB

KEGG

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

This server is last updated at February 03 2025 10:26:51.

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

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