NMR spectrum reconstruction as a pattern recognition problem

Jahangiri, Amir; Han, Xiao; Lesovoy, Dmitry M.; Agback, Tatiana; Agback, Peter; Achour, Adnane; Orekhov, Vladislav Yu.

doi:10.1016/j.jmr.2022.107342

Cited by 14 publications

(8 citation statements)

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“…We used simulated and experimental spectra to verify the performance of the LRD methodology. The one-bond couplings occur between adjacent 13 C atoms, e.g. in proteins C a -C b backbone pairs or between methyl carbons, and their adjacent carbons.…”

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confidence: 99%

“…We present here a new decoupling methodology, named LRD, which is based on the low-rank Hankel model. The onebond coupling between adjacent 13 C atoms was taken as an example for the validation of our approach and for comparison with other already established methods. The obtained decoupling results, on both synthetic and experimental spectra, demonstrate that the LRD method is capable of the decoupling, offering higher resolution and significantly cleaner spectra.…”

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confidence: 99%

“…In multidimensional NMR experiments, this forces the use of very long total measurement time, which is proportional to the number of points for indirect spectral dimensions. However, the appearance of non-uniform sampling (NUS) and reconstruction methods, such as maximum entropy, 6,7 compressed sensing (CS), 8 multi-dimensional decomposition (MDD), 9,10 low-rank Hankel method (LR) and more recently deep learning-based techniques, [11][12][13] have greatly alleviated this problem.The homo-nuclear J-coupling causes signal splitting and thus represents another reason for line-broadening and loss of resolution. The decoupling can be achieved in several ways, including the use of the pure shift approach, 14,15 constant time evolution, 16,17 bilinear rotational decoupling, 18,19 etc.The mechanism of the J-coupling is well understood and the coupling values are known.…”

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confidence: 99%

“…20,21 This information can be exploited to perform decoupling by software deconvolution also known as virtual decoupling (VD). 11,13,[22][23][24] Decoupling and reconstruction of spectrum from NUS data can be therefore combined and solved by one single method. Furthermore, it was noted that VD is likely to improve NUS reconstruction, because it reduces the number of individual peaks in the spectrum, which can have related implications for different reconstruction algorithms.…”

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confidence: 99%

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confidence: 99%

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Resolution enhancement of NMR by decoupling with the low-rank Hankel model

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Resolution enhancement of NMR by decoupling with the low-rank Hankel model

et al. 2023

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Revisiting aliasing noise to build more robust sparsity in nonuniform sampling 2D‐NMR

Cullen

Marchiori

Rovnyak

2023

Magnetic Reson in Chemistry

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A continuing priority is to better understand and resolve the barriers to using nonuniform sampling (NUS) in challenging small molecule 2D NMR with subsampling of the Nyquist grid (a.k.a. coverage) below 50%. Possible causes for artifacts, often termed sampling noise, in 1D-NUS of 2D-NMR are revisited here, where weak aliasing artifacts are a growing concern as NUS becomes sparser. As NUS schedules become sparser, repeat sequences are shown to occur in the dense sampling regions early in the sampling schedule, causing aliasing artifacts in resulting spectra. An intuitive screening approach that detects patterns in sampling schedules based on a convolutional filter was implemented. Sampling schedules that have low proportions of repeat sequences show significantly reduced artifacts. Another route to remediate early repeat sequences is a short period of uniform sampling at the beginning of the schedule, which also leads to a significant suppression of unwanted sampling noise. Combining the repeat sequence filter with a survey of HSQC and LR-HSQMBC experiments, it is shown that very short initial uniform regions of about 2%-4% of the sampling space can ameliorate repeat sequences in sparser NUS and lead to robust spectral reconstructions by iterative soft thresholding (IST), even when the point spread function is unchanged. Using the principles developed here, a suite of 'one-click' schedules was developed for broader use.

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Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes

et al. 2023

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The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few “significant” points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to “conventional” compressed sensing. We exemplify the concept of “difference CS” with one such case—the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.

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NMR spectrum reconstruction as a pattern recognition problem

Cited by 14 publications

References 50 publications

Resolution enhancement of NMR by decoupling with the low-rank Hankel model

Resolution enhancement of NMR by decoupling with the low-rank Hankel model

Revisiting aliasing noise to build more robust sparsity in nonuniform sampling 2D‐NMR

Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes

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