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.
To run PhosFox, you need the following software and inputs:
Perl version 5.6 or newer. Most Unixes and unix-like operating systems (GNU/Linux, BSDs, OS X) have this already installed. For Microsoft Windows we recommend Strawberry Perl, or the precompiled binary executable (see Installation below).
Protein sequences in FASTA format. UniProt and NCBI RefSeq FASTA formats are supported.
Detected peptide lists in plain text format. These usually come from proteomics analysis software such as ProteinPilot or Mascot. See the manual for details for supported file types. At least one case file and one control file is required.
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:
Move phosfox
into an appropriate binary directory, such as
/usr/local/bin
.
Ensure that the system Perl has Object::Tiny
, JSON
, and
Text::CSV
modules installed. They are available in
CPAN.
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.
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.
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.
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 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.