Accurate Retention Time Prediction Based on Monolinked Peptide Information to Confidently Identify Cross-Linked Peptides

Cross-linking mass spectrometry methods have not been successfully applied to protein-protein interaction discovery at a proteome- wide level mainly due to the computation complexity (O (n(2))) issue. In a previous report, we proposed a decision tree searching strategy (DTSS), which can reduce complexity by orders of magnitude. In this study, we further found that the monolinked peptides carry out the information on the retention time of the corresponding cross-linked pairs; therefore, the retention time of cross-linked peptide pairs can be predicted accurately. By utilizing the retention time as an extra filter, the false positive rate can be reduced by around 86% with a sensitivity loss of 10%. The method combined with DTSS (T-DTSS) not only benefits improving identification confidence but also leads to lower cutoff scores and facilitates substantially increasing inter-cross-link identification. T-DTSS was successfully applied to the identification of inter-cross-links obtained from Escherichia coli cell lysate cross-linked by a newly synthesized enrichable crosslinker, pDSBE. The approach can be applicable to both cleavable and noncleavable methods.

Automated summary

The study found that monolinked peptides carry information on the retention time of corresponding cross-linked pairs, enabling accurate prediction of retention time for cross-linked peptide pairs. By using retention time as an additional filter, false positive rate can be reduced significantly. The T-DTSS method not only improves identification confidence for protein-protein interactions but also increases the number of inter-cross-links identified.