a Bruker Avance-III spectrometer, operating at 600.29 MHz (1H), equipped with a 5 mm, TCI, Z-gradient Cryo-probe. 1H NMR spectra of urine were acquired using standard 1D pulse sequences
with water presaturation during both the relaxation delay (RD = 2
s) and mixing time (tm = 150 ms).42 (link) The 90° pulse length was 10 μs and total acquisition
time 2.73 s. Per sample, 64 scans were collected into 32K data-points
using a spectral width of 20 ppm. Free induction decays (FIDs) were
multiplied by an exponential weighing function (corresponding to line
broadening of 0.3 Hz) prior to Fourier-transformation.
FIDs
were referenced to an internal standard (trimethylsilyl-[2H4]-propionate, TSP), baseline and phase-corrected using
in-house software. Spectral regions containing water/urea (δ6.4
to 4.5), TSP (δ0.2 to −0.2), and noise (δ0.5 to
0.2, δ-0.2 to −4.5, δ15.5 to 9.5) were removed
prior to median-fold change normalization.43 (link) Remaining variables were binned to 7100 variables using bin widths
of 0.001 ppm to down-sample the total number of variables (for computation)
while still retaining peak shapes. A separate study44 (link) showed good analytical reproducibility of the data set
with 96% of split pairs correctly identified. Metabolic outliers were
defined, and excluded, as participants whose principal component analysis
scores, for either visit, mapped outside Hotelling’s T2 95% confidence interval (CI95).41 (link)Subset optimization by reference matching45 (link) (STORM) was used to identify metabolites using
the correlation structure
of 1H NMR data. Localized clustering of small spectral
regions was used for selecting appropriate reference spectra. Additionally,
a Bruker compound library, internal databases, and extensive 2D NMR
identification strategies46 (link) were used for
identification of molecular species.