Luciphor 2

Luciphor2 performs PTM-site localization on MS/MS data. It implements the algorithm originally described in Fermin et al. 2014 but expands it to work on any post-translational modification.

The original Luciphor program is still available at

Luciphor2 has several features over the previous version:

  • It can run on any computer that uses JAVA
  • It can score any PTM
  • It can score results from any search tool (Click here for details)
  • Like the original Luciphor, this release can process PeptideProphet XML files (pepXML). It can also read in tab-delimited files with scores from any protein search tool.

    Getting the program

  • Download the latest stable release
  • You can get the latest development code here

  • Running Luciphor2

    Luciphor2 takes a simple text file as input. To generate a template file for you to edit type the following command:

    java -jar luciphor2.jar -t

    This will create a commented text file in the current directory called lucxor_input_template.txt. This template file is preconfigured for phospho-site localization.
    Open this file in your favorite editor and adjust the parameters for your needs. All options are documented in the template file.

    After configuring the input file, feed it back into luciphor2.jar:

    java -jar luciphor2.jar input_file.txt


    If you are having problems with the software, please submit a post to the support forum or email at:


    Copyright 2014 Damian Fermin

    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

    Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.