PhosFox

PhosFox performs a peptide-level protein post-translational modification (PTM) comparison between case and control settings. It detects which peptides have been uniquely modified (for example, uniquely phosphorylated) in case and control samples, and writes the differences into HTML-formatted report files. Peptides and proteins can be also written into separate files for further analyses. Both qualitative and quantitative data sets can be analyzed. Peptide lists originating from different search engines can be also compared.

If you are not familiar with the concepts and the process, please read Söderholm et al. first.

This README file describes the software requirements and installation instructions.

Requirements

To run PhosFox, you need the following software and inputs:

Installation

If you have a working Perl, download and extract the distribution package (tar.gz, zip). All the required Perl modules are included in the package. After extraction, you should be able to run PhosFox simply by typing

phosfox job-file.json

where job-file.json is the job file that specifies the input files and parameters for the analysis. See the user manual for details. The distribution includes a job file template job.json, which you can modify to suit your case.

For Windows platforms we have compiled a binary executable phosfox.exe. It should work in both 32-bit and 64-bit Windows. The executable is stand-alone: no separate Perl environment nor any extra libraries are needed.

In Unix, you may want to install PhosFox system-wide. The following steps should be enough:

  1. Move phosfox into an appropriate binary directory, such as /usr/local/bin.

  2. Ensure that the system Perl has Object::Tiny, JSON, and Text::CSV modules installed. They are available in CPAN.

  3. Move the FIMM and PhosFox modules (in lib directory) to some directory in the Perl library path. Typically /usr/local/lib/site_perl/ is one such directory.

Post-translational modification databases

PhosFox can optionally detect novel acetylations and phosphorylations. To use this feature, you have to separately download and install database files. See DATABASES.md for instructions.

Mercurial repository

If you want to track the latest developments, you can clone the source code repository using Mercurial. See https://bitbucket.org/phintsan/phosfox/src. You will additionally need to clone FIMM module repository from https://bitbucket.org/phintsan/fimm.

User manual

The user manual is available in HTML and PDF formats. The same files are included in the distribution package. After installation, typing perldoc phosfox should also display the user manual.

Copyright

Copyright 2013, 2014 Petteri Hintsanen petterih@iki.fi

This program is free software; you may redistribute it and/or modify it under the same terms as Perl itself.