<?xml version="1.0" encoding="UTF-8"?>
<!-- Copyright 2025 Filippo Rusconi <msxpertsuite@msxpertsuite.org> -->
<component type="desktop-application">
  <id>org.msxpertsuite.minexpert3</id>
  <metadata_license>CC-BY-SA-4.0</metadata_license>
  <project_license> GPL-3.0-or-later</project_license>
  <name>MsXpS mass spectrometry software</name>
  <summary>Visualize, explore and analyze MS^n mass spectrometry data</summary>

  <developer_name>Filippo Rusconi</developer_name>

  <icon type="stock">Minexpert3</icon>

  <description>

    <p>

      MineXpert (currently MineXpert3) is a program used to visualize and
      explore MS^n mass spectral data, like mass spectra or ion mobility
      spectra.

    </p>

    <p>The program can be summarized thusly:</p>

    <ul>

      <li>Simultaneously open any number of [mzML/timsTOF]-formatted mass spec
        data files. Load a mass spectrum from the clipboard, as an [x
        y]-formatted file. Receive mass spectra from the MineXpert3 program via
        the network;
      </li>

      <li>The program computes the TIC chromatogram on MS1 acquisition data and
        fills-in a table with descriptive information of each and all the mass
        spectra in the acquisition. From there, the user starts the data
        exploration session by integrating the TIC/table view data into mass
        spectra, ion mobility spectra and various color map types;
      </li>

      <li>Any number of mass spectral data integrations (combinations) can be
        performed in any
        direction (from mass spectrum to ion mobility spectrum, or to XIC
        chromatogram, or to m/z vs ion mobility color map, for example);
      </li>

      <li>Navigation through the data is intuitive, as each new integration
        result is displayed in a composite widget that is stacked in the window
        reserved for the kind of data. There is a window for all the mass
        spectra, one for all the TIC/XIC chromatograms, one for the ion
        mobility spectra, windows for each kind of color map...;
      </li>

      <li>The software contains a JavaScript scripting interface that can be
        used to automate a number of tasks.
      </li>

    </ul>

  </description>

  <categories>
    <category>Science</category>
    <category>Education</category>
  </categories>

  <keywords>
    <keyword>Mass spectrometry</keyword>
    <keyword>Mass spectrum</keyword>
    <keyword>Ion mobility spectrum</keyword>
    <keyword>Data visualization</keyword>
    <keyword>Data exploration</keyword>
    <keyword>Mass data navigation</keyword>
    <keyword>Mass data integrations/combinations</keyword>
    <keyword>m/z binning configuration</keyword>
    <keyword>Graphics file export</keyword>
  </keywords>

  <url type="homepage">http://www.msxpertsuite.org/minexpert/</url>
  <url type="help">http://www.msxpertsuite.org/minexpert/user-manual/</url>
  <url type="contact">http://www.msxpertsuite.org/contact/contact/</url>
  <url type="vcs-browser">https://codeberg.org/MsXpertSuite/MineXpert</url>

  <launchable type="desktop-id">org.msxpertsuite.MineXpert3.desktop</launchable>

  <releases>
    <release version="all">
      <description>This page lists all the releases. Check the tags also.</description>
      <url>https://codeberg.org/MsXpertSuite/MineXpert/releases</url>
      <issues>
        <issue url="https://codeberg.org/MsXpertSuite/MineXpert/issues"></issue>
      </issues>
    </release>
  </releases>

  <provides>
    <binary>MineXpert3</binary>
  </provides>

  <screenshots>

    <screenshot type="default">
      <caption>One mass spectrometry file opened with corresponding TIC
        chromatogram and multiple XIC chromatogram (left). Mass spectra
        integrated from the TIC/XIC chromatograms (top right). Ion mobility
        spectra integrated from the TIC/XIC chromatograms (bottom right)
      </caption>
      <image>
        http://www.msxpertsuite.org/images/minexpert/general-integration-workflow.png
      </image>
    </screenshot>

    <screenshot>
      <caption>Color map shows ion mobility mass data</caption>
      <image>
        http://www.msxpertsuite.org/images/minexpert/all-three-kinds-color-maps.png
      </image>
    </screenshot>

    <screenshot>
      <caption>The trace plots and color map plots are all conveniently
        organized in defined windows. There is a window where all the TIC/XIC
        chromatograms are plotted, one where all the mass spectra are plotted,
        one for the ion mobility traces, etc. Noteworthy, the color code allows
        one to follow the integration-generated traces/maps easily even if
        multiple mass spectrometry files are loaded in the program.
      </caption>
      <image>
        http://www.msxpertsuite.org/images/minexpert/composite-plot-widget.png
      </image>
    </screenshot>

    <screenshot>
      <caption>When there are no MS1 data, the program allows the user to
        start the analysis session from a table view that documents the
        MS^n mass spectra stored in the mass spectrometry file. From there,
        it is possible to integrate the data to any other kind of
        trace/color map (button at the bottom)
      </caption>
      <image>
        http://www.msxpertsuite.org/images/minexpert/tableview-of-dataset.png
      </image>
    </screenshot>

  </screenshots>

  <suggests>
    <id>org.msxpertsuite.massxpert3</id>
  </suggests>

  <update_contact>msxpertsuite@msxpersuite.org</update_contact>

  <references>
    <doi>doi: 10.1021/acs.jproteome.9b00099</doi>
    <registry name="MEDLINE">30950277</registry>
    <doi>doi: 10.1021/jasms.0c00402</doi>
    <registry name="MEDLINE">33683899</registry>
  </references>

</component>
