NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR
-
Published:2021-11-25
Issue:2
Volume:2
Page:843-861
-
ISSN:2699-0016
-
Container-title:Magnetic Resonance
-
language:en
-
Short-container-title:Magn. Reson.
Author:
Pustovalova Yulia, Delaglio Frank, Craft D. Levi, Arthanari Haribabu, Bax Ad, Billeter Martin, Bostock Mark J., Dashti Hesam, Hansen D. Flemming, Hyberts Sven G., Johnson Bruce A., Kazimierczuk Krzysztof, Lu Hengfa, Maciejewski Mark, Miljenović Tomas M., Mobli MehdiORCID, Nietlispach Daniel, Orekhov Vladislav, Powers Robert, Qu Xiaobo, Robson Scott Anthony, Rovnyak David, Wagner Gerhard, Ying Jinfa, Zambrello Matthew, Hoch Jeffrey C.ORCID, Donoho David L., Schuyler Adam D.ORCID
Abstract
Abstract. Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform.
Funder
National Institutes of Health National Institute of Diabetes and Digestive and Kidney Diseases Australian Research Council National Science Foundation Nebraska Center for Integrated Biomolecular Communication
Publisher
Copernicus GmbH
Reference56 articles.
1. Amstutz, P., Crusoe, M. R., Tijanić, N., Chapman, B., Chilton, J., Heuer,
M., Kartashov, A., Kern, J., Leehr, D., Ménager, H., Nedeljkovich, M.,
Scales, M., Soiland-Reyes, S., and Stojanovic, L.: Common Workflow Language,
v1.0, figshare [data set], https://doi.org/10.6084/m9.figshare.3115156.v2, 2016. a 2. Barna, J. C. and Laue, E. D.: Conventional and exponential sampling for 2D
NMR experiments with application to a 2D NMR spectrum of a protein,
J. Magn. Reson., 75, 384–389,
https://doi.org/10.1016/0022-2364(87)90047-3, 1987. a 3. Billeter, M. and Orekhov, V.: Novel sampling approaches in higher dimensional
NMR, vol. 316, Springer Science & Business Media, Heidelberg, https://doi.org/10.1007/978-3-642-27160-1, 2012. a 4. Bodenhausen, G. and Ernst, R.: The accordion experiment, a simple approach to
three-dimensional NMR spectroscopy, J. Magn. Reson., 45,
367–373, 1981. a 5. Bostock, M. and Nietlispach, D.: Compressed sensing: Reconstruction of
non-uniformly sampled multidimensional NMR data, Concepts Magn.
Reson. A, 46, e21438, https://doi.org/10.1002/cmr.a.21438, 2017. a, b
Cited by
5 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|