How To Install tandem-mass on Ubuntu 18.04
Introduction
In this tutorial we learn how to install tandem-mass on Ubuntu 18.04.
What is tandem-mass
tandem-mass is:
X! Tandem can match tandem mass spectra with peptide sequences, in a process that is commonly used to perform protein identification.
This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at http://www.thegpm.org/docs/X_series_output_form.pdf.
Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used.
There are three methods to install tandem-mass on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install tandem-mass Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install tandem-mass using apt-get by running the following command:
sudo apt-get -y install tandem-mass
Install tandem-mass Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install tandem-mass using apt by running the following command:
sudo apt -y install tandem-mass
Install tandem-mass 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 tandem-mass using aptitude by running the following command:
sudo aptitude -y install tandem-mass
How To Uninstall tandem-mass on Ubuntu 18.04
To uninstall only the tandem-mass package we can use the following command:
sudo apt-get remove tandem-mass
Uninstall tandem-mass And Its Dependencies
To uninstall tandem-mass and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove tandem-mass
Remove tandem-mass Configurations and Data
To remove tandem-mass configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge tandem-mass
Remove tandem-mass configuration, data, and all of its dependencies
We can use the following command to remove tandem-mass configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge tandem-mass
References
Summary
In this tutorial we learn how to install tandem-mass package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
