topdiff command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

topdiff: command not found

or when using sudo you get the following error message

sudo: topdiff: command not found

Solutions to topdiff: command not found

How To Fix topdiff: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu topdiff is provided by toppic package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install toppic

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install toppic.

sudo apt -y install toppic

Or if you have aptitude installed you can use the following command.

sudo aptitude install toppic

Summary

In this tutorial we learn how to fix topdiff command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.