Abstract
MathIOmica‐MSViewer is an add‐on graphical user interface utility for the Mathematica software system which facilitates the visualization and exploration of spectra from open format mass spectrometry files (mzXML and mzML standard community formats). The viewer was designed for simplicity and handling of large mass spectrometry data files. To facilitate searches, users may use search filters for the spectra based on mass to charge ratios and retention times, and visualize precursor spectra associated to a parent spectrum. Availability: The viewer is available as a Mathematica notebook (MathIOmica‐MSViewer.nb) at https://doi.org/10.5281/zenodo.321385. The software is provided under an MIT License. © 2017 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons, Ltd.
Highlights
The rapid advancements of mass spectrometry have led to the increased availability of mass spectrometry data, especially in the fields of proteomics and metabolomics
To the best of our knowledge, no standalone versions exist in the Wolfram Language, which is the coding language used in the Mathematica[24] software, besides embedded functionality in the program MathDAMP,[25] originally aimed at metabolomics analysis
In this Application Note, we describe the release of MathIOmicaMSViewer, a mass spectrometry spectral viewer designed for simplicity, stability and speed, and distributed as an standalone add-on to the MathIOmica[26] package[27] for Mathematica
Summary
The rapid advancements of mass spectrometry have led to the increased availability of mass spectrometry data, especially in the fields of proteomics and metabolomics. There are few dedicated viewers, written in various programming languages: omniSpect,[19] for MATLAB, mMass3,[20] written in Python, MS-Viewer,[21] which is web based, jmzReader,[22] which offers a Java library for parsing spectra files, and BatMass,[23] which presents an updated Java implementation and interface, and is probably the most efficient of the above, in terms of quickly parsing large files.[23] To the best of our knowledge, no standalone versions exist in the Wolfram Language, which is the coding language used in the Mathematica[24] software, besides embedded functionality in the program MathDAMP,[25] originally aimed at metabolomics analysis In this Application Note, we describe the release of MathIOmicaMSViewer, a mass spectrometry spectral viewer designed for simplicity, stability and speed, and distributed as an standalone add-on to the MathIOmica[26] package[27] for Mathematica. It is offered as a supplement to existing viewers, extending the existing repertoire to users of Mathematica and the Wolfram Language
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