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

1. Install "toppic" package

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


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                toppic
            
                    
    
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2. Uninstall "toppic" package

This guide covers the steps necessary to uninstall toppic on Ubuntu 21.10 (Impish Indri):


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

Package: toppic
Architecture: amd64
Version: 1.3.0+dfsg1-4build1
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: The Debichem Group
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 18443
Depends: libboost-filesystem1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libboost-thread1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libhts3 (>= 1.10), libpwizlite3 (>= 3.0.3), libqt5core5a (>= 5.15.1), libqt5gui5 (>= 5.0.2) | libqt5gui5-gles (>= 5.0.2), libqt5widgets5 (>= 5.2.0~alpha1), libstdc++6 (>= 9), libxerces-c3.2, toppic-common (= 1.3.0+dfsg1-4build1)
Filename: pool/universe/t/toppic/toppic_1.3.0+dfsg1-4build1_amd64.deb
Size: 2341152
MD5sum: d5b3ea886ebca7827388db28251103da
SHA1: 757ee5183aa37b510b6f3b0a11095c47ac0e3f7a
SHA256: f81b580838ea03755991fdcb3cbe4ee015fad22afb2569eb9a589b158e330cd1
SHA512: 177d6b89f92a09e4c8b79e27afa7fbc58d6904d65cb14b614a49d2954feb74d449c1110df00521b08881a1aa0a79aa23002d2bb5a97bbb38c78d5417132f4d12
Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html
Description-en: Top-down proteoform identification and characterization (programs)
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.
Description-md5: ae3f1b96c71d884df9b96659eacd01d6