mzapy: An Open-Source Python Library Enabling Efficient Extraction and Processing of Ion Mobility Spectrometry-Mass Spectrometry Data in the MZA File Format

Analysis of ion mobility spectrometry (IMS) data hasbeen challengingand limited the full utility of these measurements. Unlike liquidchromatography-mass spectrometry, where a plethora of toolswith well-established algorithms exist, the incorporation of the additionalIMS dimension requires upgrading existing computational pipelinesand developing new algorithms to fully exploit the advantages of thetechnology. We have recently reported MZA, a new and simple mass spectrometrydata structure based on the broadly supported HDF5 format and createdto facilitate software development. While this format is inherentlysupportive of application development, the availability of core librariesin popular programming languages with standard mass spectrometry utilitieswill facilitate fast software development and broader adoption ofthe format. To this end, we present a Python package, mzapy, for efficient extraction and processing of mass spectrometry datain the MZA format, especially for complex data containing ion mobilityspectrometry dimension. In addition to raw data extraction, mzapy contains supporting utilities enabling tasks includingcalibration, signal processing, peak finding, and generating plots.Being implemented in pure Python and having minimal and largely standardizeddependencies makes mzapy uniquely suited to applicationdevelopment in the multiomics domain. The mzapy packageis free and open-source, includes comprehensive documentation, andis structured to support future extension to meet the evolving needsof the MS community. The software source code is freely availableat https://github.com/PNNL-m-q/mzapy.

Automated summary

We have developed mzapy, a Python package for efficient extraction and processing of mass spectrometry data, especially for complex data containing ion mobility spectrometry dimension. It includes supporting utilities for tasks such as calibration, signal processing, peak finding, and generating plots. The package is free and open-source and is structured to support future extensions to meet the evolving needs of the MS community.