pyproteome

Python library for analyzing mass spectrometry proteomics data.

Installation

To install the core pyproteome python library, install Python >= 3.6 and the latest version of pip. Then run the following command:

pip install pyproteome

To install dependencies for PHOTON, run the following command:

pip install pyproteome[photon]

Windows

If you are using Windows, it is easiest to use the latest version of Anaconda for your Python installation, as pyproteome requires several hard-to-install packages, such as NumPy and SciPy.

Then, you can simply run the above pip install pyproteome command to install this package and the rest of its dependencies.

CAMV

pyproteome can use CAMV for data validation. If you have the executable installed on your system, simply add "CAMV.exe" to your system path and pyproteome will locate it automatically.

Examples

There are several example analyses located in the pyproteome-data repository.

For a full list of package functionality, refer to the online documentation.

Directory Hierarchy

pyproteome expects a certain directory hierarchy in order to import data files and interface with CAMV. This pattern is as follows:

base_directory/
    CAMV Output/
    Figures/
    MS RAW/
    Searched/

See pyproteome.paths if you are using a custom directory hierarchy. i.e.:

>>> from pyproteome import paths
>>> paths.MS_RAW_DIR = "path/to/raw_files/"
>>> paths.MS_SEARCHED_DIR = "path/to/msf_files/"