Metabolomics aims to study the downstream effects of variables like diet, environment, or disease on a given biological system. However, inconsistencies in sample preparation, data acquisition/processing protocols lead to reproducibility and accuracy concerns. A systematic study was conducted to assess how sample preparation methods and data analysis platforms affect metabolite susceptibility. A targeted panel of 25 metabolites was evaluated in 69 clinical metabolomics samples prepared following...
[NMR paper] NMR Precision Metabolomics: Dynamic Peak Sum Thresholding and Navigators for Highly Standardized and Reproducible Metabolite Profiling of Clinical Urine Samples
NMR Precision Metabolomics: Dynamic Peak Sum Thresholding and Navigators for Highly Standardized and Reproducible Metabolite Profiling of Clinical Urine Samples
Metabolomics, especially urine-based studies, offers incredible promise for the discovery and development of clinically impactful biomarkers. However, due to the unique challenges of urine, a highly precise and reproducible workflow for NMR-based urine metabolomics is lacking. Using 1D and 2D non-uniform sampled (NUS) ¹H-^(13)C NMR spectroscopy, we systematically explored how changes in hydration or specific gravity (SG) and pH can...
nmrlearner
Journal club
0
05-24-2024 04:50 PM
Xplor-NIH: Better parameters and protocols for NMR protein structure determination
Xplor-NIH: Better parameters and protocols for NMR protein structure determination
Abstract
The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular structure determination package. In combination with an improved treatment of selected non-bonded interactions between atoms three bonds apart, such as those involving methyl hydrogens, and a previously developed term that affects the system's gyration volume, the new parameters are tested using structure calculations on 30 proteins with restraints derived from nuclear...
nmrlearner
Journal club
0
03-24-2024 06:32 AM
[NMR paper] Xplor-NIH: Better parameters and protocols for NMR protein structure determination
Xplor-NIH: Better parameters and protocols for NMR protein structure determination
The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular structure determination package. In combination with an improved treatment of selected non-bonded interactions between atoms three bonds apart, such as those involving methyl hydrogens, and a previously developed term that affects the system's gyration volume, the new parameters are tested using structure calculations on 30 proteins with restraints derived from nuclear...
More...
nmrlearner
Journal club
0
03-24-2024 06:32 AM
[NMR paper] Detection of Lung Cancer via Blood Plasma and (1)H-NMR Metabolomics: Validation by a Semi-Targeted and Quantitative Approach Using a Protein-Binding Competitor
Detection of Lung Cancer via Blood Plasma and (1)H-NMR Metabolomics: Validation by a Semi-Targeted and Quantitative Approach Using a Protein-Binding Competitor
Metabolite profiling of blood plasma, by proton nuclear magnetic resonance (¹H-NMR) spectroscopy, offers great potential for early cancer diagnosis and unraveling disruptions in cancer metabolism. Despite the essential attempts to standardize pre-analytical and external conditions, such as pH or temperature, the donor-intrinsic plasma protein concentration is highly overlooked. However, this is of utmost importance, since several...
nmrlearner
Journal club
0
08-27-2021 03:49 PM
[NMR paper] Evaluating Amber force fields using computed NMR chemical shifts.
Evaluating Amber force fields using computed NMR chemical shifts.
Related Articles Evaluating Amber force fields using computed NMR chemical shifts.
Proteins. 2017 Jul 08;:
Authors: Koes DR, Vries JK
Abstract
NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations....
nmrlearner
Journal club
0
07-09-2017 11:44 PM
[NMR paper] Non-targeted 1H-NMR-metabolomics suggest the induction of master regulators of energy metabolism in the liver of vitamin E-deficient rats.
Non-targeted 1H-NMR-metabolomics suggest the induction of master regulators of energy metabolism in the liver of vitamin E-deficient rats.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles Non-targeted 1H-NMR-metabolomics suggest the induction of master regulators of energy metabolism in the liver of vitamin E-deficient rats.
Food Funct. 2015 Apr;6(4):1090-7
Authors: Moazzami AA, Frank S, Gombert A, Sus N, Bayram B, Rimbach G, Frank J
Abstract
nmrlearner
Journal club
0
03-02-2016 07:20 PM
Protocols and applications of cellular metabolomics in safety studies using precision-cut tissue slices and carbon 13 NMR.
Protocols and applications of cellular metabolomics in safety studies using precision-cut tissue slices and carbon 13 NMR.
Protocols and applications of cellular metabolomics in safety studies using precision-cut tissue slices and carbon 13 NMR.
Methods Mol Biol. 2011;691:205-25
Authors: Baverel G, Renault S, Faiz H, El Hage M, Gauthier C, Duplany A, Ferrier B, Martin G
Numerous xenobiotics are toxic to human and animal cells by interacting with their metabolism, but the precise metabolic step affected and the biochemical mechanism behind such a...
Evaluating protocols for reproducible targeted metabolomics by NMR
Linear Mode
