Luciphor is a program that performs phospho-site localization on MS/MS data processed by the Trans-Proteomic Pipeline (TPP). It is the first phospho-site prediction program to provide estimates for the false localization rate (FLR).

Luciphor takes in as input PeptideProphet XML files and spectral files (mzXML, mzML). From these it predicts the correct phosopho-peptide permutation for the peptide sequences reported in the XML files.

  • Download the latest stable release
  • Download the mzXML files used in the original publication
  • Get instructions on how to compile the source code
  • Get a description of the commandline options
  • Get a description of the output produced by Luciphor
  • You can get the latest development code here.

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

    Luciphor is written in C++ and uses the Boost and MS-ToolKit for reading mz*ML files. Instructions for compiling Luciphor locally on your computer are provided here This software is designed to be compiled and executed on Linux. All testing has been performed on RHEL 6.4 (64-bit), GCC compiler version 4.4.7 20120313.


    Copyright 2013 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.