TopPIC Suite


TopPIC Suite consists of five software tools for the analysis of top-down mass spectrometry data: TopFD, TopIndex, 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 isotopic envelopes and converts isotopic envelopes to monoisotopic neutral masses. In addition, it extracts proteoform features from LC-MS or CE-MS data.
  • TopIndex (Top-down protein sequence database Indexing) generates index files for protein sequence databases. The index files are used in TopPIC and TopMG to speed up proteoform identification by database search.
  • 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, generating 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 highly 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.

Release notes

Version 1.6 (December 10, 2022)
  • [TopPIC] Added support for variable PTMs.
  • [TopPIC] Rewrote protein sequence filtering functions.
Version 1.5 (December 3, 2021)
  • [TopFD] Added support for FAIMS data.
  • [TopPIC] Rewrote the localization function.
Version 1.4 (December 30, 2020)
  • [TopFD] Added multiple thread support.
  • [TopIndex] Added TopIndex.
Version 1.3 (December 31, 2019)
  • [TopPIC] Added spectral visualization using Html files.
  • [TopMG] Added spectral visualization using Html files.
  • [TopDiff] Added TopDiff.
Version 1.2 (November 15, 2018)
  • [TopFD] Added support for processing multiple files
  • [TopFD] Optimized the code to speed up computation
  • [TopPIC] Added support for data containing multiple fractions
  • [TopMG] Added TopMG
Version 1.1 (November 15, 2017)
  • [TopFD] Added TopFD
  • [TopFD] Added a GUI wrapper topfd_gui
  • [TopPIC] Added a filtering method based on proteoform-level FDR
  • [TopPIC] Added a GUI wrapper toppic_gui
Version 1.0 (May 26, 2016)
  • [TopPIC] Added the support for spectral pairs or triplets generated by the alternating fragmentation mode
  • [TopPIC] Optimized the algorithms for protein filtering and spectral alignment
  • [TopPIC] Added the MIScore method for mass shift characterization
Version 0.9 (December 8, 2014)
  • [TopPIC] First release