TopPIC Suite

Summary

TopPIC Suite consists of two software tools for the interpretation of top-down mass spectrometry data: TopFD and TopPIC.

  • 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 envelops to monoisotopic neutral masses. In addition, it extracts proteoform features from MS1 spectra.
  • TopPIC (Top-down mass spectrometry based Proteoform Identification and Characterization) identifies and characterizes proteoforms at the whole 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 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 its speed, sensitivity, and accuracy.

Release notes

Version 1.1.0 (November 15, 2017)
  • [TopFD] Added TopFD
  • [TopFD] Added a GUI wrapper topfd_gui for TopFD
  • [TopPIC] Added a filtration method based on proteoform-level FDR
  • [TopPIC] Added a GUI wrapper toppic_gui for TopPIC
Version 1.0.0 (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 0.9.0 (December 8, 2014)
  • [TopPIC] First release