An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR

Abstract

Non-uniform weighted sampling (NUWS) is a sampling strategy, related to nonuniform sampling (NUS) in the limit of long acquisition times, in which each indirect increment of a multidimensional spectrum is sampled multiple times according to some weighting function. As the spectrum is fully sampled it can be processed in a conventional manner by the discrete Fourier transform, making the analysis of sensitivity much more straightforward than for NUS data. Previously, 2-3 fold increases in signal-to-noise ratio (SNR) have been reported using NUWS. However, as the sampling schedule acts as a window function, the observed SNR must be compared with uniformly sampled data apodized using the same weighting function. On doing this, we calculate more modest improvements of 10-20% in SNR, and these are verified experimentally for spectra of α-synuclein and YFP. Nevertheless, we prove that NUWS always improves the sensitivity compared with identically processed uniformly sampled data, and when combined with rapid recycling experiments such as the SOFAST-HMQC, NUWS methods have the potential to make a useful and practical contribution to sensitivity-limited measurements.

Structural characterization of the interaction of α-synuclein nascent chains with the ribosomal surface and trigger factor

“…The limited solubility of RNC samples together with the observed NMR line broadening resulted in very weak signal intensities, equivalent to just 50-100 nM concentrations of isolated αSyn. Nevertheless, a combination of methodological advances, including longitudinal relaxation optimized experiments and nonuniform weighted sampling (35,36), have enabled quantitative measurements to be made of CSs and cross-peak intensities for the majority of NC residues. Most importantly, a combination of biochemical and noninvasive spectroscopic assays were applied to ensure that all NMR signals analyzed in this study arise from intact, ribosomebound NCs (Fig.…”

“…NMR data were acquired at 4°C on a 700-MHz Bruker Avance III spectrometer with TXI cryoprobe. The 1 H-15 N SOFAST-HMQC (35) spectra were recorded using nonuniform weighted sampling (36). 15 N-XSTE and 1 H stimulated echo (STE) diffusion experiments were acquired using a diffusion delay of 100 ms and bipolar trapezoidal gradient pulses (total length, 4 ms; shape factor, 0.9) with strengths of 0.028 and 0.532 Tm −1 .…”

Sensitivity of Nonuniform Sampling NMR

“…In this report, NUS means the samples are selected from the Nyquist grid and are each acquired with the same number of transients, but NUS has been further generalized with respect to sample phases, 14 while a strategy of acquiring different numbers of transients on the uniform grid 10 has been revisited. 15,16 …”

Performance tuning non-uniform sampling for sensitivity enhancement of signal-limited biological NMR

“…Dynamic nuclear polarization promises to transform studies of biological solids, while microcoil and cryogenic probe technologies permit challenging multi-dimensional spectroscopy on unprecedented mass-sensitivities on the order of 1–100 μg for important small molecules such as natural products and metabolites (Hilton and Martin 2010). Continued instrumentation innovations can be expected to yield more returns on improving signal detection, but recent work has shed light on extending the detection limit of multi-dimensional NMR spectroscopy by non-uniform sampling (NUS) (Rovnyak et al 2011; Paramasivam et al 2012; Waudby and Christodoulou 2012; Qiang 2011; Kumar et al 1991; Hyberts et al 2010, 2013). Specifically, for the case of NUS of selecting a subset of samples (termed a sampling schedule) from a uniform Nyquist grid, exact theory and experimental verifications show that NUS data of decaying signals experience an enhanced intrinsic signal-to-noise ratio ( i SNR) on the order of up to two fold over uniformly sampled data in the same experimental time (Rovnyak et al 2011; Paramasivam et al 2012).…”

“…Subsequently, enhanced SNR by NUS in indirect evolution periods was described for the practice of acquiring all indirect increments uniformly but with a non-uniform distribution of the number of transients (Kumar et al 1991) a practice sometimes termed non-uniform weighted sampling (NUWS) which is seeing renewed interest (Waudby and Christodoulou 2012; Qiang 2011). Estimates of SNR enhancements were later refined by the exact solution (Rovnyak et al 2011).…”