toppic - 1.3.0+dfsg1-4+b1 main

The TopPIC Suite consists of four software tools for the interpretation
of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff.
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-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.
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-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.
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-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.
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-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.