Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK.
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.
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
JM
Würz
Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany. guentert@em.uni-frankfurt.de.|Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland. guentert@em.uni-frankfurt.de.|Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan. guentert@em.uni-frankfurt.de.
Peter
0000-0002-2911-7574
P
Güntert
D000465:Algorithms; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008962:Models, Theoretical
Automated assignment; CYANA; Contour lines; Peak list; Peak picking; Structure calculation