An automated peak picking method. PICKY adapts a brand noise estimation method to efficiently estimate the noise. It consists of four sequential steps: noise-level estimation, forming and sub-dividing the components, peak picking, peak pruning and refinement. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking.