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Pipeline publication

[…] R) at monthly time points., A total of 43 samples were prepared and analysed using nuclear magnetic resonance (NMR) and ultra high pressure liquid chromatography (UPLC)–mass spectrometry (MS)/MS analytical platforms as described in online supplementary material. Frozen sera were obtained from the Division of Rheumatology, Allergy and Immunology at UC San Diego School of Medicine (San Diego, California, USA) for polar and lipid analyses. NMR spectra were acquired with a 16.4 T (700 MHz) Bruker Avance spectrometer (Bruker BioSpin, Billerica, Massachusetts, USA) equipped with a 5 mm TCI cryogenically cooled probe and an autosampler at 30°C. Following acquisition, spectra were processed using NMRlab and MetaboLab. Metabolite assignment and quantification were performed using several database. , UPLC–MS analysis on lipid fraction was performed on a Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer equipped with an Accela 1250 pump and an autosampler as described in online supplementary material (Thermo Scientific, Waltham, Massachusetts, USA). Metabolite assignment was performed at a 5 ppm mass accuracy range by interrogation of several databases. MetaboAnalyst V.3.0 and VANTED software were used for metabolic pathway analysis (see online supplementary material)., Partial least squares discriminant analysis (PLSDA) with venetian blinds cross-validation was performed using PLS-Toolbox (Eigenvector Research, Manson, Washington, USA). Polar metabolite correlation relationships were reported in Pearson's correlation coefficients and visualised as a heat map with hierarchical clustering analysis with Euclidean distance metric by MATLAB. Statistical significance analysis between responders and non-responders was performed using an unpaired Student's t-test (statistical significance: *p<0.1, **p<0.05 and ***p<0.01)., After 6 months […]

Pipeline specifications

Software tools NMRLab, Metabolab, MetaboAnalyst