A decision tree searching strategy to boost the identification of cross-linked peptides

We describe an efficient decision tree searching strategy (DTSS) to boost the identification of cross-linked peptides. The DTSS approach allows the identification of a wealth of complementary information to facilitate the construction of more protein-protein interaction networks for human cell lysate, which was tested by the use of a recently reported cross-linking dataset (ACS Cent. Sci. 2019, 5, 1514−1522). A variant of the PhoX-linker, named pDSPE was synthesized and applied to cross-link E.coli cell lysate to demonstrate that the acquisition of doubly charged ions can significantly improve identifica-tion results. The method can be seamlessly integrated to other search engines to maximize the number of identified cross-links