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mineXpert2: Full-Depth Visualization and Exploration of MSn Mass Spectrometry Data

  • Olivier Langella
    Olivier Langella
    PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
  •  and 
  • Filippo Rusconi*
    Filippo Rusconi
    PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
    *Email: [email protected]. Phone: +33 (0)1 69 33 23 54. Fax: +33 (0)1 69 33 23 40.
Cite this: J. Am. Soc. Mass Spectrom. 2021, 32, 4, 1138–1141
Publication Date (Web):March 8, 2021
https://doi.org/10.1021/jasms.0c00402
Copyright © 2021 American Society for Mass Spectrometry. Published by American Chemical Society. All rights reserved.

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    Abstract

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    mineXpert is a mass spectrometric data visualization and exploration software supporting only MS1 data that is aimed at proteomics scientists who do rarely require manual MS/MS data visualization and exploration (Rusconi, F. J. Proteome Res.2019, 18, 2254–2259). In order to adapt it to new use cases in our facility and to widen its user base, mineXpert was entirely rewritten with the main aim of implementing MSn data support. Other feature additions were new data visualization and exploration methods, with an overhaul of the data plotting code to allow more flexible uses of mass data integration results. Further, the whole mass spectral data set can now be explored in a table view where the user may filter the data using a number of criteria that can be logically combined to pinpoint the smallest feature of interest. Ion mobility mass spectrometry is supported with specific data exploration and plotting. With mineXpert2, we provide a software program that will be of use to all mass spectrometrists, without restrictions on the field of endeavor, from pure chemistry to proteomics and metabolomics. As staff members of a mass spectrometry facility, we want to provide all users with a mass spectrometry data visualization and exploration software solution that frees them from the need to use closed-source vendor software. After conversion of the mass data to mzML, mineXpert2 requires no proprietary software whatsoever. The reference implementation is version 7.0.0 or greater. The software, a detailed user manual, and video tutorials are available at http://www.msxpertsuite.org.

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    • Detailed user manual for mineXpert2 (PDF)

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    Cited By

    This article is cited by 4 publications.

    1. Henri Voedts, Constantin Anoyatis-Pelé, Olivier Langella, Filippo Rusconi, Jean-Emmanuel Hugonnet, Michel Arthur. (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nature Microbiology 2024, 9 (3) , 647-656. https://doi.org/10.1038/s41564-024-01609-w
    2. Henri Voedts, Sean P. Kennedy, Guennadi Sezonov, Michel Arthur, Jean-Emmanuel Hugonnet. Genome-wide identification of genes required for alternative peptidoglycan cross-linking in Escherichia coli revealed unexpected impacts of β-lactams. Nature Communications 2022, 13 (1) https://doi.org/10.1038/s41467-022-35528-3
    3. Heiner Atze, Yucheng Liang, Jean-Emmanuel Hugonnet, Arnaud Gutierrez, Filippo Rusconi, Michel Arthur. Heavy isotope labeling and mass spectrometry reveal unexpected remodeling of bacterial cell wall expansion in response to drugs. eLife 2022, 11 https://doi.org/10.7554/eLife.72863
    4. Henri Voedts, Delphine Dorchêne, Adam Lodge, Waldemar Vollmer, Michel Arthur, Jean‐Emmanuel Hugonnet. Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross‐linking enzymes in Escherichia coli. The EMBO Journal 2021, 40 (19) https://doi.org/10.15252/embj.2021108126

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