ECL: An Exhaustive Search Tool for the Identification of Cross-Linked Peptides Using Whole Database (Deprecated)

About ECL

ECL is short for Exhaustive Cross-Linked peptides identification.

Has been deprecated. Please use ECL2.
Where to download ECL and how to use it?

Executable file can be downloaded from: https://github.com/fcyu/ECL/releases.

Source code: https://github.com/fcyu/ECL

Requirement: Java version >= 1.7.

Usage: 

java -Xmx25g -jar ECL.jar parameter.def data_file.mzXML

parameter.def: Parameter file. Can be download along with ECL.

data_file.mzXML: Spectra data file (mzXML).

For any enquiry, please contact Fengchao Yu at fyuab@connect.ust.hk

Example spectra and database

Cross-linking of two synthetic peptides: ECL_try.zip

Usage instruction:

    Download ECL_try.zip and ECL.zip.
    Unzip them and put everything to a folder. For example "D:\ECL_try\".
    Edit the parameter.def. Make sure that the paths of "db" is correct.
    Open the command window, and type 
    java -Xmx32g -jar D:\ECL_try\ECL.jar D:\ECL_try\parameter.def D:\ECL_try\XL_midK.mzXML
    The result files will be in the "D:\ECL_try\".
    You can use any directory. Remember to change the directories accordingly.
About ECLViewer (a replacement of ECLAnnotator)

ECLViewer is a software viewing ECL results.
Where to download ECLAnnotator and how to use it?

Executable file: https://bioinformatics.hkust.edu.hk/ecl/ECLViewer.zip

Requirement: Microsoft .NET Framework 4.5.2 link.

Usage: Unzip "ECLVIewer.zip", and double-click "ECLViewer.exe". The spectra file should be MGF format (converted by TPP or ProteoWizard)

For any enquiry, please contact Fengchao Yu at fyuab@connect.ust.hk
Related Publication
Fengchao Yu, Ning Li*, Weichuan Yu*. *Joint corresponding authors.
"ECL: An Exhaustive Search Tool for the Identification of Cross-Linked Peptides Using Whole Database".
BMC Bioinformatics, 17:1-8, 2016, [link]