consists of two software tools for the interpretation of top-down mass
spectrometry data: TopFD and TopPIC.
(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.
(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.
Version 1.1.0 (November 15, 2017)
Version 1.0.0 (May 26, 2016)
- [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 0.9.0 (December 8, 2014)
- [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