MINEXPERT2(1)

💖 mineXpert2 — the manual page, but make it a vibe 💖

okay bestie, so this is mineXpert2, and it lives in section 1 of the General Commands Manual. she opens your mass spec data files, she shows them off, she lets you mine them like the main character you are. 🧚✨

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✨ NAME ✨

mineXpert2 — open mass spectrometric data files of a wide variety of formats, visualize and mine data graphically

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✨ SYNOPSIS ✨

minexpert2 [options]  [filename ...]

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✨ DESCRIPTION ✨

This manual page documents briefly the mineXpert2 software.

This program can be used to load mass spectrometry data files and show the spectral data in a variety of graphical representations like plots, color maps. Any plot or color map can serve as a starting point for a mass data integration, like integrating a region of a TIC chromatogram to a mass spectrum or to a drift spectrum. 🦋

Integrations can be performed in any direction, like from a RT|MZ color map to a TIC chromatogram, for example, or from a drift spectrum to a TIC chromatogram.

The mineXpert2 program allows the user to perform the following tasks:

• Open mass spectrometry data files (mzML, mzXML, asc, xy, ...);
• Display in a table view the full data set, for easy filtering;
• Calculate and display the TIC chromatogram;
• Calculate and display a mz=f(rt) color map;
• For mobility data, calculate and display a mz=f(dt) color map;
• Integrate the mass spectrometric data from any kind of data representation (mass | drift spectra, TIC | XIC chromatogram, JD color maps) to any other kind of data representation;
• For any mass data feature (mass peak, TIC | XIC peak, color map) integrate to a XIC single intensity value);
• Powerful isotopic cluster calculation starting from a chemical formula, optionally with user-defined isotopic abundance ratios;
• Gaussian fit over any isotopic cluster to estimate the average mass of a given ion;
• Mouse-driven deconvolution of m/z data (charge envelope-based or isotopic cluster-based);
• Export the data to text files;
• Export the graphical representation of mass spectrometric data to graphics files of a number of formats (jpg, png, pdf).

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✨ OPTIONS ✨

• -h | --help — Displays detailed usage information and exits. it's giving "help me help you" 🫶
• -c | --config — Display program configuration at build time and the Qt version used to build it.
• -V | --Version — Print the version of the software program along the with version of the Qt libraries used to build it.
• -l | --license — Print the license of this software.
• -s | --streamed — When opening one or more files in the gui, do that in streamed mode, otherwise in full.
• -j | --scriptFile <filename> — Start the program and immediately run the JavaScript script.
• filename ... — One or more names of files to be opened.

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📚 Bibliographic reference to be cited

Not yet published...

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👀 See also

• massxpert (1)

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🌸 Useful reading

The program is documented fully in the mineXpert2 User Manual, that is packaged in msxpertsuite-doc. That manual is available in the form of a PDF-formatted file (/usr/share/doc/msxpertsuite/minexpert2-doc.pdf).

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👑 AUTHOR

Filippo Rusconi <lopippo@debian.org>

This manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 03 july 2017). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation.

On a Debian system the complete text of the GNU General Public License version 3 can be found in the file /usr/share/common-licenses/GPL-3.

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and that's the whole page, bestie 💅✨ so anyway, this whole thing is filed under section 1 in the General Commands Manual — that's the footer tea, and the source/version bit up top was a lil placeholder, no cap. go read your data, you icon, periodt. 🎀💖🌈