[Debichem-devel] Bug#961085: ITP: toppic -- Top-down proteoform identification and characterization

[Filippo Rusconi]

Source: toppic
Section: science
Priority: optional
Maintainer: The Debichem Group <debichem-devel at lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo at debian.org>
Build-Depends: debhelper-compat (= 12),
               dpkg-dev (>= 1.18.25),
               cmake (>= 3.12)
Standards-Version: 4.5.0
Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html
Vcs-Browser: https://salsa.debian.org/debian/toppic
Vcs-Git: https://salsa.debian.org/debian/toppic.git

Package: wnpp
Severity: wishlist
Owner: Filippo Rusconi <lopippo at debian.org>

~~~~
I intend to package the toppic software that is necessary to perform mass
spectrometry-based protein identifications. 

This software will become essential in my own laboratory research, along with
other software packages that I created and that I already maintain with the
debichem team.

I will maintain the package within the debichem team.

Package: toppic
Architecture: any
Depends: ${shlibs:Depends}, 
         ${misc:Depends}
Description: Top-down proteoform identification and characterization
 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.

Regards,

Filippo

-- 

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄⠀⠀⠀⠀  http://msxpertsuite.org
          http://www.debian.org