How To Install toppic on Debian 12

Learn how to install toppic on Debian 12 with this tutorial. toppic is Top-down proteoform identification and characterization (programs)

Introduction

In this tutorial we learn how to install toppic on Debian 12.

What is `toppic`

toppic is:

The TopPIC Suite consists of four software tools for the interpretation of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff.

-TopFD (Top-down mass spectral Feature Detection) is a software tool for top-down spectral deconvolution and a successor to MS-Deconv. It groups top-down spectral peaks into isotopomer envelopes and converts isotopomer envelopes to monoisotopic neutral masses. In addition, it extracts proteoform features from LC-MS or CE-MS data.

-TopPIC (Top-down mass spectrometry based Proteoform Identification and Characterization) identifies and characterizes proteoforms at the proteome level by searching top-down tandem mass spectra against a protein sequence database. TopPIC is a successor to MS-Align+. It efficiently identifies proteoforms with unexpected alterations, such as mutations and post-translational modifications (PTMs), accurately estimates the statistical significance of identifications, and characterizes reported proteoforms with unknown mass shifts. It uses several techniques, such as indexes, spectral alignment, generation function methods, and the modification identification score (MIScore), to increase the speed, sensitivity, and accuracy.

-TopMG (Top-down mass spectrometry based proteoform identification using Mass Graphs) is a software tool for identifying ultra-modified proteoforms by searching top-down tandem mass spectra against a protein sequence database. It is capable of identifying proteoforms with multiple variable PTMs and unexpected alterations, such as histone proteoforms and phosphorylated ones. It uses mass graphs, which efficiently represent candidate proteoforms with multiple variable PTMs, to increase the speed and sensitivity in proteoform identification. In addition, approximate spectrum-based filtering methods are employed for protein sequence filtering, and a Markov chain Monte Carlo method (TopMCMC) is used for estimating the statistical significance of identifications.

-TopDiff (Top-down mass spectrometry-based identification of Differentially expressed proteoforms) compares the abundances of proteoforms and finds differentially expressed proteoforms by using identifications of top-down mass spectrometry data of several protein samples.

There are three methods to install toppic on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install toppic Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install toppic

Install toppic Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install toppic

Install toppic 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

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

sudo aptitude -y install toppic

How To Uninstall toppic on Debian 12

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

sudo apt-get remove toppic

Uninstall toppic And Its Dependencies

To uninstall toppic and its dependencies that are no longer needed by Debian 12, we can use the command below:

sudo apt-get -y autoremove toppic

Remove toppic Configurations and Data

To remove toppic configuration and data from Debian 12 we can use the following command:

sudo apt-get -y purge toppic

Remove toppic configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge toppic

Dependencies

toppic have the following dependencies:

References

Summary

In this tutorial we learn how to install toppic package on Debian 12 using different package management tools: apt, apt-get and aptitude.