Bug#961085: ITP: toppic -- Top-down proteoform identification and characterization
Maintainer: The Debichem Group <firstname.lastname@example.org>
Uploaders: Filippo Rusconi <email@example.com>
Build-Depends: debhelper-compat (= 12),
dpkg-dev (>= 1.18.25),
cmake (>= 3.12)
Owner: Filippo Rusconi <firstname.lastname@example.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
I will maintain the package within the debichem team.
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
- 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.
⢀⣴⠾⠻⢶⣦⠀ Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁ Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀ Debian Developer