Computational protocol: Nitrite Derived from Endogenous Bacterial Nitric Oxide Synthase Activity Promotes Aerobic Respiration

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Protocol publication

[…] The collected supernatants were lyophilized and reconstructed in NMR buffer (potassium phosphate buffer in D2O, pH 7.4 [uncorrected], with 500 mM trimethylsilyl propanoic acid [TMSP] as an internal standard). 2D 1H-13C HSQC spectra were collected on a Bruker Avance III-HD 700-MHz spectrometer equipped with a quadrapole-resonance QCI-P cryoprobe (1H, 13C, 15N, and 31P), a SampleJet automated sample changer, Bruker ICON-NMR, and an automatic tuning and matching (ATM) unit. NMRPipe () and NMRViewJ () were used to process and analyze the collected spectra. The TMSP internal standard was used for chemical shift referencing and normalization of NMR peak intensities. NMR peaks from the 2D 1H-13C HSQC spectra were annotated by comparing the observed 1H and 13C chemical shifts to the metabolite reference data from the Platform for RIKEN Metabolomics (PRIMe) (), Human Metabolome Database (HMDB) (), Madison metabolomics Consortium Database (), Metabominer (), and BiomagResBank (BMRB) () with error tolerances of 0.08 ppm and 0.25 ppm for 1H and 13C chemical shifts, respectively. The relative intensity (i.e., concentration) of each metabolite was calculated by averaging the intensities of all NMR peaks unambiguously assigned to the metabolite. […]

Pipeline specifications

Software tools NMRPipe, NMRViewJ, MetaboMiner
Application NMR-based metabolomics
Organisms Bacteria, Staphylococcus aureus
Diseases Drug-Related Side Effects and Adverse Reactions
Chemicals Nitric Oxide