A fast and exhaustive cross-linked peptides identification tool.
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README.md

ECL2

ECL2 is an advanced version of ECL. It has a linear computational complexity. It also supports multi-thread computation and multiple variable modifications.

How to use it?

Requirements: Java 1.8.

Download the ECL2-2.1.7.zip from the latest release page https://github.com/fcyu/ECL2/releases/latest/ and unzip the file.

Usage:

java -Xmx128g -jar /path/to/ECL2.jar <parameter_file> <data_file>
  1. <parameter_file>: parameter file. Can be downloaded along with ECL2.
  2. <data_file>: spectra data file (mzXML or MGF).

Example: java -Xmx128g -jar ECL2.jar parameter.def data.mzxml

Cite

Yu, Fengchao, Ning Li, and Weichuan Yu. "Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity." Journal of Proteomics Research 16.10 (2017): 3942-3952.

[bibtex]

@article{yu2017exhaustively,
  title={Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity},
  author={Yu, Fengchao and Li, Ning and Yu, Weichuan},
  journal={Journal of Proteome Research},
  volume={16},
  number={10},
  pages={3942--3952},
  year={2017},
  publisher={ACS Publications}
}