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

About Xolik

Identifying cross-linked peptides requires huge computing resources to exhaustively search all pairwise combinations of peptides in a large database. Commonly used heuristic screening strategies reduce the number of candidate pairs during the identification. However, heuristic screening strategies may miss true findings. We propose a novel linear-time algorithm to exhaustively search all peptide pairs within an acceptable period of time.

Here we implement a novel linear-time matching algorithm for finding cross-linked peptides in Xolik. We use a modified XCorr score as the default scoring function. Xolik can identify cross-linked peptides from mzXML/mzML data files. Details about the method are in the paper below.

Related Publication
J. Dai*, W. Jiang*, F. Yu* and W. Yu. *These authors contributed equally to this work.
"Xolik: finding cross-linked peptides with maximum paired scores in linear time",
Bioinformatics, 35(2): 251-257, 2018.

Where to download Xolik

The source code and binaries are available at: (updated Apr. 20, 2018)
Source code:       Xolik_src.zip (Downloads = )
Windows 64-bit:  Xolik_win64.zip (Downloads = )
Linux 64-bit:        Xolik_linux64.zip (Downloads = )

Environment configuration

Please install Python 2.7 and pandas for separately controlling FDR on intra/inter-protein PSMs.

How to use it?

To run Xolik, please use the following commands.

./Xolik -d db-filename.fasta -s msdata-filename.mzXML -o output-filename.csv --ms1tol 5 --ms2tol 0.02
python splitctrl.py output-filename.csv

Please use ./Xolik --help for all available options.

For any enquiry, please contact DAI, Jiaan ( jdaiab@connect.ust.hk).

Test data

Please redirect to MXDB for the synthetic disulfide-bridged dataset for testing purpose.

Random databases used in the paper are at random_databases.zip.