PICKY: a novel SVD-based NMR spectra peak picking method

Abstract

Motivation: Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly.

Results: We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 A.

Availability: PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking.

Fig. 1.

Noise reduction using SVD for a 2D component in the ¹⁵N-HSQC spectrum: (a) the original component of two highly overlapping peaks, (b) the reconstruction of (a) by the vectors, corresponding to the largest singular value.

Fig. 2.

Illustration of PICKY performance on the 2D ¹⁵N-HSQC spectrum of YST0336. All the data points with intensities >1.5 × 10⁵, which is automatically determined by PICKY, are set to grey. Peaks are shown by the black dots. Some strong peaks, caused by side chains, are filtered by cross-referencing.

Fig. 3.

(a) The correlation between decoy quality in terms of RMSD value to the crystal structure, and ¹⁵N-edited NOESY contact score. The blue point on y-axis represents the crystal structure, which has higher contact score than any decoy does. (b) The superimposition between the decoy selected by ¹⁵N-edited NOESY contacts, which is also the best decoy (shown in cyan), and the crystal structure of TM1112 (shown in magenta). Backbone RMSD is 1.25 Å.