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 (n2)) 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 cross-linker, pDSBE. The approach can be applicable
to both cleavable and noncleavable methods.