Apr 29, 2024

Public workspacecosy_metab.nan

Forked from a private protocol
DOI
dx.doi.org/10.17504/protocols.io.eq2lyw3zpvx9/v1
  • 1Network for Advanced NMR;
  • 2University of Georgia
  • Saraa Al Jawad: Protocol review;
  • Christopher Esselman: Protocol review
  • Leandro I Ponce: Protocol review
NAN support at UGA
Open access
DOI: dx.doi.org/10.17504/protocols.io.eq2lyw3zpvx9/v1
Protocol Citation: NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison 2024. cosy_metab.nan. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2lyw3zpvx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 08, 2024
Last Modified: April 29, 2024
Protocol Integer ID: 97923
Keywords: NAN, NMR, Metabolomics, COSY
Funders Acknowledgement:
National Science Foundation
Grant ID: 194670
Disclaimer
This protocol is developed and maintained by Network for Advanced NMR (NAN). The protocol content here is for informational purposes only and does not constitute legal, medical, clinical, or safety advice, or otherwise; content added to this protocol is not peer reviewed and may not have undergone a formal approval of any kind. Information presented in this protocol should not substitute for independent professional judgment, advice, diagnosis, or treatment. Any action you take or refrain from taking using or relying upon the information presented here is strictly at your own risk. You agree that neither the Company nor any of the authors, contributors, administrators, or anyone else associated with this protocol, can be held responsible for your use of the information contained in or linked to this protocol or any of our Sites/Apps and Services.
Abstract
This is a protocol for running the Bruker pulse program "cosygpprqf" for metabolomics samples.
Guidelines
This protocol intends to provide concise instructions to carry out the experiment. For more comprehensive information, see Bruker's documentation "Basic NMR Experiments" by clicking ? → Manuals (docs) on the menu bar on TopSpin. See also "Pulse Program Catalogue. 1D/2D" for the details about the pulse program used in this protocol.
Before start
This protocol assumes:
  • Your sample is loaded, locked, tuned, and shimmed in the magnet
  • The calibrated 90° pulse value for proton (i.e., P1) for the sample has been collected
Create a new dataset
Create a new dataset

On the menu bar on TopSpin, click on
Start → Create Dataset
(This protocol uses TopSpin 3.6.4, and the interface may look different on other TopSpin versions.)

Note
You can also use the new command in the command line to do this step.

Enter
  • NAME: Name of a set of datasets (e.g., human_serum_study1). Use a single string.
  • EXPNO: Dataset number. Use a positive integer.

Select
  • Directory: Your directory.


Note
Your new dataset will be stored in Directory/NAME/EXPNO

Select
Read parameterset

Click the button
Select
A new window opens. On the right top bar, select
Source = /opt/NAN_METAB/par

In the list, select the one you want to use:

For serum and plasma samples:
  • COSY_br600_serum.par: Parameter set optimized for serum samples.

For urine samples:
  • COSY_br600_urine.par: Parameter set optimized for urine samples.
  • COSY_NUS_br600_urine.par: Parameter set using an acquisition mode "non-uniform sampling (NUS)". Higher resolution on the indirect dimension

Note
Parameter set names in the list vary between spectrometers
(e.g., COSY_br800_serum.par).

Click
OK
Click
OK
Go to the "USE DEFAULT" tab below to proceed with the default optimized parameters.
Step case

Use default parameters:
6 steps

This step case uses the default optimized parameters to acquire a spectrum.

Load the calibrated P1 using the following command in the command line.

getprosol 1H [calibrated P1 value] [power level for P1]
(e.g., getprosol 1H 10.01 -7.45)

Note
[power level for P1] varies between spectrometers. Never use a wrong [power level for P1].

Critical
Click on
Acquire → Gain
in the menu bar to automatically set the receiver gain.


Note
You can also use the rga command in the command line.

Click
Go
in the menu bar to acquire a spectrum.
Note
You can also use the zg command in the command line.

After the run, click on
Process → Proc. Spectrum
in the menu bar to execute an automated processing macro.


If you want to modify parameters to improve your spectrum, go to step 2 and move to the step case "MODIFY PAR".