Retention time as an extra dimension for proteome-wide cross-link identification
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ABSTRACT: Chemical crosslinking methods have not been successfully applied to protein-protein interaction discovery mainly due to the computation complexity (O (n2)) issue. In a previous report, we proposed a decision tree searching strategy which can reduce complexity by orders of magnitude. In this study, we found that the mono-linked peptides carry out the information of the retention time of the cross-linked pairs, therefore the retention time of cross-linked peptide pairs can be predicted accurately. By utilizing the obtained retention time information, the false positive rate can be reduced by around 86% with a sensitivity loss of 12%. The method was successfully applied to the identification of inter cross-links obtained from E. coli cell lysate crosslinked by a newly synthesized enrichable crosslinker.
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Bos Taurus (bovine) Escherichia Coli
TISSUE(S): Blood Plasma, Cell Culture
SUBMITTER: Hongli Chen
LAB HEAD: Hongli Chen
PROVIDER: PXD024253 | Pride | 2021-07-29
REPOSITORIES: Pride
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