Aug 16, 2023

Public workspacesample_prep_urine.nan

Forked from a private protocol
DOI
dx.doi.org/10.17504/protocols.io.j8nlkowkwv5r/v1
  • 1Network for Advanced NMR (NAN);
  • 2University of Georgia
  • Leandro I Ponce: Protocol review;
  • Saraa Al Jawad: Protocol review
NAN support at UGA
Open access
DOI: dx.doi.org/10.17504/protocols.io.j8nlkowkwv5r/v1
Protocol Citation: NAN KB, Mario Uchimiya, John Glushka, Leandro I Ponce, Saraa Al Jawad, Laura Morris, Arthur Edison 2023. sample_prep_urine.nan. protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlkowkwv5r/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: August 03, 2023
Last Modified: August 16, 2023
Protocol Integer ID: 85925
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and does not constitute legal, medical, clinical, or safety advice, or otherwise; content added to this protocol is not peer reviewed and may not have undergone a formal approval of any kind.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 modified protocol for NMR metabolomics for urine samples. This method was originally proposed by:
CITATION
Dona AC, Jiménez B, Schäfer H, Humpfer E, Spraul M, Lewis MR, Pearce JT, Holmes E, Lindon JC, Nicholson JK (2014). Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping.. Analytical chemistry.
LINK
https://doi.org/10.1021/ac5025039
See also:

CITATION
Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS (2015). Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.. Metabolomics : Official journal of the Metabolomic Society.
LINK
https://link.springer.com/article/10.1007/s11306-014-0746-7



Materials
1. Chemicals and reagents
  • Phosphate buffer in D2O (1.5 M, pH 7.4, 1.11 mM DSS-d6)

2. Equipment
  • Calibrated micropipettes (100 μL, 200 μL, and 1000 μL)
  • Pippette tips
  • 1.5-mL Eppendorf tubes
  • 5-mm SampleJet NMR tubes from Bruker
  • Centrifuge
  • Vortex mixer

3. Study samples
  • Urine samples
Before start
This protocol assumes that the original urine samples have >600 µL.
7m 10s
7m 10s
Day-1/1
Thaw samples TemperatureOn ice or at Temperature4 °C
Centrifuge the samples at Temperature4 °C at Centrifigation12000 x g for Duration00:05:00 min

Note
  • This step is to remove particles in the samples
  • Sample tube and volume specifications vary depending on the study


5m
Centrifigation
Add Amount60 µL of the phosphate buffer to Amount540 µL of the supernatant for each sample

  • Use 1.5-mL Eppendorf tubes
Pipetting
Critical
Vortex the samples at Temperature4 °C for Duration00:02:00
2m
Centrifuge the samples at Temperature4 °C for Duration00:00:10



Note
This step is to remove samples attached to tube caps, and no centrifugation speed specified

10s
Centrifigation
Transfer Amount590 µL of the supernatant to an NMR tube for each sample
Note
No stickers/labels on the caps and tubes allowed


Citations
Dona AC, Jiménez B, Schäfer H, Humpfer E, Spraul M, Lewis MR, Pearce JT, Holmes E, Lindon JC, Nicholson JK. Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping.
https://doi.org/10.1021/ac5025039
Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.
https://link.springer.com/article/10.1007/s11306-014-0746-7