toppic

Top-down proteoform identification and characterization (programs)

Description

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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