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}
}