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Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK

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Abstract

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.

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Acknowledgements

We thank Torsten Herrmann for providing NOESY spectra and peak lists produced by ATNOS for the CASD-NMR proteins, Piotr Klukowski for providing peak lists produced by the CV-Peak Picker software, and Fred Damberger for helpful discussions. We gratefully acknowledge financial support by the Lichtenberg program of the Volkswagen Foundation, a Grant-in-Aid for Scientific Research of the Japan Society for the Promotion of Science (JSPS), and a Eurostars grant by the Swiss Confederation.

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Authors and Affiliations

  1. Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany

    Julia M. Würz & Peter Güntert

  2. Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland

    Peter Güntert

  3. Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan

    Peter Güntert

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  1. Julia M. Würz
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Correspondence to Peter Güntert.

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Würz, J.M., Güntert, P. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK. J Biomol NMR 67, 63–76 (2017). https://doi.org/10.1007/s10858-016-0084-3

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