Complete Guide: Installing toppic-common on Ubuntu 21.10 (Impish Indri) 2024

1. Install "toppic-common" package

Please follow the steps below to install toppic-common on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                toppic-common
            
                    
    
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2. Uninstall "toppic-common" package

This is a short guide on how to uninstall toppic-common on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                toppic-common
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the toppic-common package on Ubuntu 21.10 (Impish Indri)

Package: toppic-common
Architecture: all
Version: 1.3.0+dfsg1-4build1
Priority: optional
Section: universe/science
Source: toppic
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: The Debichem Group
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 24344
Depends: fonts-font-awesome, fonts-freefont-ttf, libjs-filesaver, libjs-bootstrap4, libjs-popper.js, libjs-jquery-ui, node-jquery
Filename: pool/universe/t/toppic/toppic-common_1.3.0+dfsg1-4build1_all.deb
Size: 5435884
MD5sum: 0fb8d65e49e39b760853615764735663
SHA1: 2737443ff85d40970d5e86fe7126231139cb36fc
SHA256: 3cea21710616f7c9ca2584c0216148599be8ad97b5d0054902c06141a5ad4c39
SHA512: a62177708689a2a84725573cf18dd759e612d9d4e439bd7edb9b784fefc207100d3a0a8a45e68d4752e288e0a4b12961bbc599e2d7b88cefd33b6ba73c3e163b
Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html
Description-en: Top-down proteoform identification and characterization (common data)
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.
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This package ships common data used by the various program in the
toppic package.
Description-md5: bbae5ecb9fcba93e79d38a482e49ed1b