consists of five software tools for the analysis of top-down mass
spectrometry data: TopFD, TopIndex, TopPIC, TopMG, and TopDiff.
(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.
(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.
(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.
Version 1.6 (December 10, 2022)
Version 1.5 (December 3, 2021)
- [TopPIC] Added support for variable PTMs.
- [TopPIC] Rewrote protein sequence filtering functions.
Version 1.4 (December 30, 2020)
- [TopFD] Added support for FAIMS data.
- [TopPIC] Rewrote the localization function.
Version 1.3 (December 31, 2019)
- [TopFD] Added multiple thread support.
- [TopIndex] Added TopIndex.
Version 1.2 (November 15, 2018)
- [TopPIC] Added spectral visualization using Html files.
- [TopMG] Added spectral visualization using Html files.
- [TopDiff] Added TopDiff.
Version 1.1 (November 15, 2017)
- [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 1.0 (May 26, 2016)
- [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 0.9 (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