EasyPQP: Simple library generation for OpenSWATH

EasyPQP is a Python package that provides simplified and fast peptide query parameter generation for OpenSWATH. It can process input from MSFragger, Sage or other database search engines in pepXML/idXML/tsv format. Statistical validation can be conducted either using PyProphet or PeptideProphet/iProphet. Retention times and ion mobilities are calibrated using an internal or external standard. In addition to a cumulative library, run-specific libraries are generated for non-linear RT alignment in OpenSWATH. For generation of PTM specific libraries that utilizes a unimod.xml database, you can further restrict the unimod.xml database file for modifications and site-specificities of interest.

Installation

We strongly advice to install EasyPQP in a Python virtualenv. EasyPQP is compatible with Python 3.

Install the development version of easypqp from GitHub:

    $ pip install git+https://github.com/grosenberger/easypqp.git@master

Running EasyPQP

EasyPQP is not only a Python package, but also a command line tool:

   $ easypqp --help

or:

   $ easypqp convert --help
   $ easypqp convertpsm --help
   $ easypqp convertsage --help
   $ easypqp library --help
   $ easypqp reduce --help
   $ easypqp filter-unimod --help
   $ easypqp openswath-assay-generator --help
   $ easypqp openswath-decoy-generator --help
   $ easypqp targeted-file-converter --help

Docker

EasyPQP is also available from Docker (automated builds):

Pull the development version of easypqp from DockerHub (synced with GitHub):

    $ docker pull grosenberger/easypqp:latest