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

About Xolik

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

Here we implement the linear-time matching algorithm for finding cross-linked peptides in Xolik. We use a modified XCorr as the default scoring function. It can be used for identifying 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. *Contributed equally to this work.
"Xolik: finding cross-linked peptides with maximum paired scores in linear time",
in preparation.

Where to download Xolik

The source code and binaries are available at:
Source code:       Xolik_src_31-May-2017.zip
Windows 64-bit:  Xolik_win64_31-May-2017.zip
Linux 64-bit:       Xolik_linux64_31-May-2017.zip

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, 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

Use ./Xolik --help for all available options.

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.