PythoMS: A Python Framework To Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data

Mass spectrometric data are copious and generate a processing burden that is best dealt with programmatically. PythoMS is a collection of tools based on the Python programming language that assist researchers in creating figures and video output that is informative, clear, and visually compelling. T...

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Bibliographic Details
Published in:Journal of chemical information and modeling 2019-04, Vol.59 (4), p.1295-1300
Main Authors: Yunker, Lars P. E, Donnecke, Sofia, Ting, Michelle, Yeung, Darien, McIndoe, J. Scott
Format: Article
Language:English
Subjects:
Biological evolution
Histograms
Mathematical analysis
Noise reduction
Programming languages
Python
Scripts
Spectrometry
Zooming
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Summary:Mass spectrometric data are copious and generate a processing burden that is best dealt with programmatically. PythoMS is a collection of tools based on the Python programming language that assist researchers in creating figures and video output that is informative, clear, and visually compelling. The PythoMS framework introduces a library of classes and a variety of scripts that quickly perform time-consuming tasks: making proprietary output readable; binning intensity vs time data to simulate longer scan times (and hence reduce noise); calculating theoretical isotope patterns and overlaying them in histogram form on experimental data (an approach that works even for overlapping signals); rendering videos that enable zooming into the baseline of intensity vs time plots (useful to make sense of data collected over a large dynamic range) or that depict the evolution of different species in a time-lapse format; calculating aggregates; and providing a quick first-pass at identifying fragments in MS/MS spectra. PythoMS is a living project that will continue to evolve as additional scripts are developed and deployed.
ISSN:1549-9596
1549-960X
DOI:10.1021/acs.jcim.9b00055