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

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