A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

Abstract We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, 15 N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking…

• NN
  National Natural Science Foundation of China

  Awards: 31470805, 21475141, 31700727
• NK
  National Key Research and Development Program of China

  Award: 2016YFA0501300