spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization

Given the wide diversity in applications of biological
mass spectrometry,
custom data analyses are often needed to fully interpret the results
of an experiment. Such bioinformatics scripts necessarily include
similar basic functionality to read mass spectral data from standard
file formats, process it, and visualize it. Rather than having to
reimplement this functionality, to facilitate this task, spectrum_utils is a Python package for mass spectrometry
data processing and visualization. Its high-level functionality enables
developers to quickly prototype ideas for computational mass spectrometry
projects in only a few lines of code. Notably, the data processing
functionality is highly optimized for computational efficiency to
be able to deal with the large volumes of data that are generated
during mass spectrometry experiments. The visualization functionality
makes it possible to easily produce publication-quality figures as
well as interactive spectrum plots for inclusion on web pages. spectrum_utils is available for Python 3.6+, includes
extensive online documentation and examples, and can be easily installed
using conda. It is freely available as open source under the Apache
2.0 license at https://github.com/bittremieux/spectrum_utils.