Spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization.

Wout Bittremieux

doi:10.1021/acs.analchem.9b04884

Wout Bittremieux

Open Access

https://doi.org/10.1021/acs.analchem.9b04884

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Abstract

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 .

Highlights

Mass spectrometry (MS) is a powerful, high-throughput analytical technique that can be used to identify and quantify molecules in complex biological samples
Peaks can be annotated with their peptide fragments, potentially including post-translational modifications (PTMs) at specified amino acid positions, molecules encoded as SMILES strings, or custom annotations
Spectrum_utils takes the MS data provided by such tools as input for subsequent processing and visualization. spectrum_utils has a well-defined, Pythonic application programming interface, allowing developers to harness its powerful functionality in a small number of lines of code

Summary

Introduction

Mass spectrometry (MS) is a powerful, high-throughput analytical technique that can be used to identify and quantify molecules in complex biological samples. Because during a typical MS experiment tens of thousands of mass spectra are generated, suitable bioinformatics tools are needed to analyze such large data volumes. MS data processing has traditionally been done using monolithic software tools that aim to provide fully end-toend solutions from the raw data to the final identification or quantification results. Instead, customized data analysis workflows are often needed to fully interpret the results of an MS experiment. In recent years several software packages for the general-purpose analysis of MS data in popular scripting languages have been developed. We present the spectrum_utils package for MS data processing and visualization in Python. Spectrum_utils allows the user to manipulate mass spectral data and quickly prototype ideas for computational MS projects. A key feature of spectrum_utils is its focus on computational efficiency to process large amounts of spectral data. A key feature of spectrum_utils is its focus on computational efficiency to process large amounts of spectral data. spectrum_utils is freely available as open source under the Apache 2.0 license at https://github.com/bittremieux/spectrum_utils

Methods & results

Conclusion