pLink2

'pLink 2' is an improved search engine for high-speed and reliable proteome-scale identification of cross-linked peptides. It employs a two-stage open search strategy with fragment indexing, making it approximately 40 times faster than its predecessor 'pLink 1' and 3-10 times faster than 'Kojak'. Systematic evaluation using various datasets and analysis methods demonstrates that 'pLink 2' surpasses ten state-of-the-art search engines in precision and sensitivity, particularly at proteome scales. Re-analysis of published datasets with 'pLink 2' significantly reduces processing time and identifies more cross-linked residue pairs compared to 'pLink 1'.