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

ABSTRACT: 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

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Escherichia Coli

SUBMITTER: Wenzhang Chen

LAB HEAD: wenzhang chen

PROVIDER: PXD018291 | Pride | 2020-11-23

REPOSITORIES: Pride

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Decision Tree Searching Strategy to Boost the Identification of Cross-Linked Peptides.

Huang Rong R Gao Xiuxia X Xu Zili Z Zhu Wei W Wei Ding D Jiang Biao B Chen Hongli H Chen Wenzhang W

Analytical chemistry 20201002 20

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 data set (ACS Cent. Sci. 2019, 5, 1514-1522). A variant of the PhoX-linker, named pDSPE, was synthesized ...[more]

PMID: 32955856

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