Application of CRAFT in two‐dimensional NMR data processing

Abstract

Two-dimensional (2D) data are typically truncated in both dimensions, but invariably and severely so in the indirect dimension. These truncated FIDs and/or interferograms are extensively zero filled, and Fourier transformation of such zero-filled data is always preceded by a rapidly decaying apodization function. Hence, the frequency line width in the spectrum (at least parallel to the evolution dimension) is almost always dominated by the apodization function. Such apodization-driven line broadening in the indirect (t ) dimension leads to the lack of clear resolution of cross peaks in the 2D spectrum. Time-domain analysis (i.e. extraction of frequency, amplitudes, line width, and phase parameters directly from the FID, in this case via Bayesian modeling into a tabular format) of NMR data is another approach for spectral resonance characterization and quantification. The recently published complete reduction to amplitude frequency table (CRAFT) technique converts the raw FID data (i.e. time-domain data) into a table of frequencies, amplitudes, decay rate constants, and phases. CRAFT analyses of time-domain data require minimal or no apodization prior to extraction of the four parameters. We used the CRAFT processing approach for the decimation of the interferograms and compared the results from a variety of 2D spectra against conventional processing with and without linear prediction. The results show that use of the CRAFT technique to decimate the t interferograms yields much narrower spectral line width of the resonances, circumventing the loss of resolution due to apodization. Copyright © 2016 John Wiley & Sons, Ltd.

Absolute Minimal Sampling in High‐Dimensional NMR Spectroscopy

“…[20] Figure 3s hows for selected residues of arginine kinase HN(CA)CO and HNCO cross sections of the full 3D FT spectra along with AMS fits (red bars in Figure 3). Ther esults show that both the peak positions and their amplitudes match very well the FT results that required over seven-times longer measurement times.This applies also for HN(CA)CO traces with multiple resonances present ( Figure 3D,E,F), despite amedian signal-to-noise ratio of the first 15 N, 1 Hp lane of only about 15:1. Thec omparison for all assigned residues of AK, which is given in the Supporting Information, demonstrates that the AMS approach produces peak lists with high accuracy and reliability in an optimal amount of time.…”

“…Thes tandard acquisition of NMR experiments in three (or higher) dimensions,however, is time intensive,taking of the order of aday or longer. Forexample, 3D NMR experiments of uniformly 15 N, 13 C-labeled protein samples are traditionally acquired by independently incrementing the evolution times t 1 and t 2 along the 13 Ca nd 15 N dimensions with N 1 and N 2 complex points,r espectively. [1,2] This approach leads to atotal acquisition time that grows with N 1 N 2 ,where N 1 and N 2 are typically set to 32-64 increments so that the spectral resolution after FT along the two indirect dimensions is sufficiently high (typically of the order of afew tens of Hz).…”

“…[11] Although this improves spectral resolution and minimizes truncation artifacts,i ti s typically limited to atwo-fold reduction in measurement time per indirect dimension. More recently,o ther time-domain fitting methods have been proposed, such as the filter diagonalization method, [12,13] the CRAFT method for the compilation of tables with frequencies,linewidths and amplitudes of signals in 1D and 2D NMR datasets, [14,15] and for am ore accurate extraction of peak amplitudes from 2D HSQC spectra. [16] Fora ll of these methods,t he absolute minimal number of increments to attain the relevant spectral information is unknown.…”

“…TheA MS approach permits accurate determination of resonance positions and amplitudes also for 3D experiments where more than one 13 C' cross-peak is present for each backbone 15 N, 1 Hf requency pair as is the case in the HN-(CA)CO experiment. [20] Figure 3s hows for selected residues of arginine kinase HN(CA)CO and HNCO cross sections of the full 3D FT spectra along with AMS fits (red bars in Figure 3).…”

Complex mixtures by NMR and complex NMR for mixtures: experimental and publication challenges

“…But robust methods have been proposed when misaligned peaks are a concern that rely on operations such as peak‐picking and signal deconvolution that are more prone to errors. Because automatic alignment is extremely challenging for severely overlapped signals and thus may introduce artefacts, an alternative challenge is to learn how to model these shifts, converting them into a valuable source of information about pH, ionic strength and matrix effects . This goal may be achieved if enough raw data are made available and may contribute to improve the reliability of automatic procedures.…”