recipe easypqp

EasyPQP: Simple library generation for OpenSWATH


Developer docs:


BSD / BSD-3-Clause



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 or other database search engines in pepXML format. Statistical validation can be conducted either using PyProphet or PeptideProphet/iProphet. Retention times 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.

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+


Running EasyPQP ===============

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


$ easypqp --help




$ easypqp convert --help $ easypqp library --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


package easypqp

(downloads) docker_easypqp



depends biopython:

depends click:

depends matplotlib-base:

depends numba:

depends numpy:

depends pandas:

depends pyopenms:

depends pyprophet:

depends python:


depends scikit-learn:

depends scipy:

depends seaborn:

depends statsmodels:

depends tqdm:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install easypqp

and update with::

   mamba update easypqp

To create a new environment, run:

mamba create --name myenvname easypqp

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `easypqp/tags`_ for valid values for ``<tag>``)

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