TopPIC Suite

TopPIC Suite is a software package for proteoform identification and quantification by top-down MS. It consists of five software tools: TopFD, TopIndex, TopPIC, TopMG, and TopDiff. TopFD is a tool for top-down spectral deconvolution, which converts complex isotopic patterns of proteoforms or proteoform fragments into their monoisotopic masses. TopIndex generates protein sequence indexes for speeding up database search of top-down mass spectra. TopPIC and TopMG identify modified proteoforms using spectral alignment and graph alignment between mass spectra and database protein sequences. TopDiff compares the abundances of proteoforms identified from multiple samples.

TopPG

TopPG is a software pipeline for proteoform identification by top-down proteogenomics which generates sample-specific protein databases by combining the RNA-seq and top-down MS data. It contains functions to generate a customized protein database with genetic variations and/or splicing variations.

TopMSV

TopMSV is a web-based tool for top-down MS data visualization. It provides various 2D and 3D views for top-down MS data. Researchers can use TopMSV to explore LC profiles, LC–MS maps, MS and MS/MS spectra, and spectral deconvolution and proteoform identification results. Developers can also use JavaScript libraries provided by TopMSV to implement their interfaces for MS data visualization.

MS-Deconv

MS-Deconv is a combinatorial algorithm for spectral deconvolution. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest-scoring subset of envelopes as the heaviest path in the graph. In contrast with other approaches, the algorithm scores sets of envelopes rather than individual envelopes.

MS-Align+

MS-Align+ is a fast algorithm for top-down protein identification based on the spectral alignment that enables searches for unexpected post-translational modifications.

MS-Align-E

MS-Align-E is a software tool for identifying ultramodified proteins with expected and unexpected PTMs using top-down mass spectrometry.

CHAMPS

CHAMPS (Complete Homology Assisted MS/MS Protein Sequencing) is a software tool for computing the complete sequence of a protein from the tandem mass spectrometry data generated from multiple enzyme digestions of the protein.

TBNovo

TBNovo is a de novo protein sequencing software tool that combines both top-down and bottom-up tandem mass spectra.

GlycoMID

GlycoMID is a graph-based spectral alignment algorithm that identifies glycopeptides with multiple glycosylation sites from tandem mass spectra.

MSBE

MSBE is a tool for the analysis of gene expression data using a new bi-clustering method. It can find constant bi-clusters and additive bi-clusters.

PPIExtend

PPIExtend is a tool for finding quasi-bicliques in Protein-Protein-Interaction (PPI) Networks.