How To Install msxpertsuite on Ubuntu 22.04
Introduction
In this tutorial we learn how to install msxpertsuite
on Ubuntu 22.04.
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 22.04. 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 22.04
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 22.04, 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 22.04 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
References
Summary
In this tutorial we learn how to install msxpertsuite
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.