RT Journal Article
SR Electronic
T1 Xolik: finding cross-linked peptides with maximum paired scores in linear time
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 155069
DO 10.1101/155069
A1 Jiaan Dai
A1 Wei Jiang
A1 Fengchao Yu
A1 Weichuan Yu
YR 2017
UL http://biorxiv.org/content/early/2017/06/24/155069.abstract
AB 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 criteria may ignore true findings.Results We directly tackle the combination challenge without using any screening strategies. With the additive scoring function and 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, and the running time of Xolik is validated using databases with different number of proteins. Experiments using synthetic and empirical datasets show that Xolik outperforms existing tools in terms of running time and statistical power.Availability Source code and binaries of Xolik are freely available at http://bioinformatics.ust.hk/Xolik.html.Contact eeyu{at}ust.hkSupplementary information Supplementary data are available at Bioinformatics online.