Xolik: Finding cross-linked peptides with maximum paired scores in linear time

Abstract

Motivation Cross-linking technique coupled with mass spectrometry (MS) is widely used in the analysis of protein structures and protein-protein interactions. In order to identify cross-linked peptides from MS data, we need to consider all pairwise combinations of peptides, which is computationally prohibitive when the sequence database is large. To alleviate this problem, some heuristic screening strategies are used to reduce the number of peptide pairs during the identification. However, heuristic screening strategies may miss some true cross-linked peptides. Results We directly tackle the combination challenge without using any screening strategies. With the data structure of double-ended queue, the proposed algorithm reduces the quadratic time complexity of exhaustive searching down to the linear time complexity. We implement the algorithm in a tool named Xolik. The running time of Xolik is validated using databases with different numbers of proteins. Experiments using synthetic and empirical datasets show that Xolik outperforms existing tools in terms of running time and statistical power. Availability and implementation Source code and binaries of Xolik are freely available at http://bioinformatics.ust.hk/Xolik.html. Supplementary informationSupplementary dataare available at Bioinformatics online.