Nature Communications (Jul 2019)

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

  • Zhen-Lin Chen,
  • Jia-Ming Meng,
  • Yong Cao,
  • Ji-Li Yin,
  • Run-Qian Fang,
  • Sheng-Bo Fan,
  • Chao Liu,
  • Wen-Feng Zeng,
  • Yue-He Ding,
  • Dan Tan,
  • Long Wu,
  • Wen-Jing Zhou,
  • Hao Chi,
  • Rui-Xiang Sun,
  • Meng-Qiu Dong,
  • Si-Min He

DOI
https://doi.org/10.1038/s41467-019-11337-z
Journal volume & issue
Vol. 10, no. 1
pp. 1 – 12

Abstract

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The identification of cross-linked peptides at a proteome scale for interactome analyses represents a complex challenge. Here the authors report an efficient and reliable search engine pLink 2 for proteome-scale cross-linking mass spectrometry analyses, and demonstrate how to systematically evaluate the credibility of search engines.