TopPIC

TopPIC Suite contains the following tools:
1. TopFD (TOP-Down Mass Spectrometry-Based Proteoform Identification and Characterization) is a tool to deconvolute spectrum grouping spectral peaks into isotopomers to monoisotopic neutral masses and to compute proteoform features from LC-MS or CE-MS data.
2. TopPIC (Top-down mass spectrometry-based Proteoform Identification and Characterization) is a tool for the identification and characterization of proteoforms by searching a protein sequence database. The TopPIC algorithm uses spectral alignment, a generation function, and indices to increase the speed.
3. TopMG (Top-down mass spectrometry-based proteoform identification using Mass Graphs) is a tool to identify ultra-modified proteoforms using protein sequence database searches in tandem mass spectra (MS/MS) data. The TopMG algorithm uses mass graphs, approximate spectrum-based filtering methods, a Markov chain Monte Carlo method, and can identify proteoforms with multiple variable PTMs and other alterations, for example, histone proteoforms and phosphorylations.
4. TopDiff (Top-down mass spectrometry-based identification of Differentially expressed proteoforms) is a tool to compare proteoform abundances and to find differentially expressed proteoforms.