Würz Julia M, Güntert Peter
Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
J Biomol NMR. 2017 Jan;67(1):63-76. doi: 10.1007/s10858-016-0084-3. Epub 2017 Feb 3.
The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity. The performance of CYPICK was evaluated for a variety of spectra from different proteins by systematic comparison with peak lists obtained by other, manual or automated, peak picking methods, as well as by analyzing the results of automated chemical shift assignment and structure calculation based on input peak lists from CYPICK. The results show that CYPICK yielded peak lists that compare in most cases favorably to those obtained by other automated peak pickers with respect to the criteria of finding a maximal number of real signals, a minimal number of artifact peaks, and maximal correctness of the chemical shift assignments and the three-dimensional structure obtained by fully automated assignment and structure calculation.
在多维核磁共振谱中自动识别信号是一项具有挑战性的任务，信号重叠、噪声和光谱伪影使其变得复杂，目前尚无普遍接受的方法。在此，我们提出一种新的峰挑选算法CYPICK，它尽可能遵循光谱学家在分析光谱等高线图中的峰模式时所采用的手动方法，但实现了完全自动化。通过对应用于等高线的几何标准进行评估，如局部极值、近似圆形（在对光谱轴进行适当缩放后）和凸性，取代了人工目视检查。通过与其他手动或自动峰挑选方法获得的峰列表进行系统比较，以及基于CYPICK输入峰列表分析自动化学位移归属和结构计算结果，对不同蛋白质的各种光谱评估了CYPICK的性能。结果表明，在找到最大数量的真实信号、最小数量的伪峰以及通过完全自动化归属和结构计算获得的化学位移归属和三维结构的最大正确性等标准方面，CYPICK生成的峰列表在大多数情况下优于其他自动峰挑选器获得的峰列表。
