A Python Package for the Localization of Protein Modifications in Mass Spectrometry Data

Determining the correct localization
of post-translational modifications
(PTMs) on peptides aids in interpreting their effect on protein function.
While most algorithms for this task are available as standalone applications
or incorporated into software suites, improving their versatility
through access from popular scripting languages facilitates experimentation
and incorporation into novel workflows. Here we describe pyAscore,
an efficient and versatile implementation of the Ascore algorithm
in Python for scoring the localization of user defined PTMs in data
dependent mass spectrometry. pyAscore can be used from the command
line or imported into Python scripts and accepts standard file formats
from popular software tools used in bottom-up proteomics. Access to
internal objects for scoring and working with modified peptides adds
to the toolbox for working with PTMs in Python. pyAscore is available
as an open source package for Python 3.6+ on all major operating systems
and can be found at pyascore.readthedocs.io.