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A fast and exhaustive cross-linked peptides identification tool.

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ECL2

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

Executable file

Download the zipped file from https://github.com/fcyu/ECL2/releases/latest.

How to use it

Requirements: Java 1.8.

How to compile from source

Download and install JDK 8 from https://www.oracle.com/java/technologies/downloads/#java8

Download Maven from https://maven.apache.org/download.cgi

Download and install ProteomicsLibrary library:

git clone https://github.com/fcyu/ProteomicsLibrary.git
cd ProteomicsLibrary
mvn install

Download and compile ECL2:

git clone https://github.com/fcyu/ECL2.git
cd ECL2
mvn package

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

An example of the result file

scan_num spectrum_id spectrum_mz spectrum_mass peptide_mass rt C13_correction charge score delta_C ppm peptide protein protein_annotation_1 protein_annotation_2 e_value q_value mgf_title
47330 47330 1215.974 3642.894 3642.889 7401 -2 3 2.136501 0.112479 1.352205 n[34.063]QLTEMKGHETK[34.063]c-6-n[34.063]EYKLTYYTPEYETK[34.063]c-3 AT5G37830.1-ATCG00490.1 Symbols: OXP1 oxoprolinase 1 chr5:15056635-15060525 REVERSE LENGTH=1266 Symbols: RBCL ribulose-bisphosphate carboxylases chrC:54958-56397 FORWARD LENGTH=479 2.79E-06 0

Explainations:

  1. scan_num: Scan num (starts from 1) of the spectrum.
  2. spectrum_id: Spectrum ID.
  3. spectrum_mz: Observed spectrum precursor MZ value.
  4. spectrum_mass: Observed neutral mass of the spectrum.
  5. peptide_mass: Theoretical mass of the identified peptide.
  6. rt: Retention time (in seconds) of the spectrum. Only applicable to mzXML format.
  7. C13_correction: The number of C13 isotope correction.
  8. charge: Precursor charge.
  9. score: Identification score. It's similar to XCorr.
  10. delta_C: The relative difference between the top score and the second best score.
  11. ppm: PPM between spectrum_mass and peptide_mass.
  12. peptide: identified peptide sequence.
  13. protein: Protein accessions.
  14. protein_annotation_1: The protein annotation of the first chain.
  15. protein_annotation_2: The protein annotation of the second chain.
  16. e_value: e-value of the peptide-spectrum match.
  17. q_value: q-value (used as FDR) of the peptide-spectrum match.
  18. mgf_title: MGF title if the spectral file is in MGF format.

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},
  doi={10.1021/acs.jproteome.7b00338}
}