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“…Experiments showed that about 30 % of these additional identified peptides were not pre-selected by Kojak. We used protein crystal structures from the protein data bank to check the intra-protein cross-linked peptides. …”
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“…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. …”
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