How To Install msxpertsuite on Ubuntu

Posted on April 1, 2023  (Last modified on May 20, 2023 )

3 minutes  • 579 words

Introduction

In this tutorial we learn how to install msxpertsuite on Ubuntu.

What is msxpertsuite

msxpertsuite is:

msXpertSuite provides programs to model linear (bio-) polymer chemistries, simulate mass spectral data, analyse and data-mine mass. It is the successor of GNU polyXmass, first, and then of massXpert.

The massXpert and mineXpert programs allow the following:

massXpert:

• making brand new polymer chemistry definitions;
• using the definitions to perform easy calculations in a desktop calculator-like manner;
• performing sophisticated polymer sequence editing and simulations;
• perform m/z list comparisons;

Chemical simulations encompass cleavage (either chemical or enzymatic), gas-phase fragmentations, chemical modification of any monomer in the polymer sequence, cross-linking of monomers in the sequence, arbitrary mass searches, calculation of the isotopic pattern…

mineXpert:

• Open mass spectrometry data files (mzML, mzXML, asc, xy, …);
• Calculate and display the TIC chromatogram;
• For mobility data, calculate and display a mz=f(dt) color map;
• Integrate the data from the TIC chromatogram or color map
  • to mass spectrum;
  • to drift spectrum;
  • back to TIC chromatogram (XIC chromatogram);
  • reverse operations;
  • to single TIC intensity value (for mass spectral intensity comparisons);
• Model centroids peaks into mass spectra using either the Gaussian model or the Lorentzian model;
• Export the data to text files;
• Slice a big initial file into smaller chunks for easier mining;
• Define how mining activity is recorded on disk for later use;
• Convert mzML files into a private (albeit open) mass spectrometry format that allows better performance (based on SQLite3).

This package depends on both massXpert and mineXpert packages and thus will install both of them. To install only one of the packages, install the corresponding msxpertsuite-massxpert or msxpertsuite-minexpert package.

There are three methods to install msxpertsuite on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install msxpertsuite Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install msxpertsuite using apt-get by running the following command:

sudo apt-get -y install msxpertsuite

Install msxpertsuite Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install msxpertsuite using apt by running the following command:

sudo apt -y install msxpertsuite

Install msxpertsuite Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install msxpertsuite using aptitude by running the following command:

sudo aptitude -y install msxpertsuite

How To Uninstall msxpertsuite on Ubuntu

To uninstall only the msxpertsuite package we can use the following command:

sudo apt-get remove msxpertsuite

Uninstall msxpertsuite And Its Dependencies

To uninstall msxpertsuite and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove msxpertsuite

Remove msxpertsuite Configurations and Data

To remove msxpertsuite configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge msxpertsuite

Remove msxpertsuite configuration, data, and all of its dependencies

We can use the following command to remove msxpertsuite configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge msxpertsuite

Dependencies

msxpertsuite have the following dependencies:

• msxpertsuite-massxpert
• msxpertsuite-massxpert
• msxpertsuite-minexpert
• msxpertsuite-minexpert

References

• msxpertsuite website

Summary

In this tutorial we learn how to install msxpertsuite package on Ubuntu using different package management tools: apt, apt-get and aptitude.