MS-Deconv

MS-Deconv performs spectral deconvolution of tandem mass spectra in top-down proteomics to resolve overlapping isotopomer envelopes and recover monoisotopic masses for intact proteins.

Key Features:

• Combinatorial algorithm: Generates and evaluates combinations of isotopomer envelopes to identify the most probable grouping of isotopic variants of protein fragments.
• Candidate isotopomer envelope generation: Produces a comprehensive set of candidate isotopomer envelopes from the input spectrum.
• Graph-based representation: Transforms spectral data into a graph where nodes correspond to isotopomer envelopes and edges represent possible transitions between them.
• Set-based scoring and heaviest path selection: Scores sets of envelopes and selects the highest-scoring subset as a heaviest path within the graph.
• Improved monoisotopic mass recovery and speed: Demonstrates improved recovery of monoisotopic masses and processing speed compared with Thrash and Xtract.

Scientific Applications:

• Top-down proteomics spectral deconvolution: Resolves complex tandem mass spectra of intact proteins to aid analysis of proteoforms and post-translational modifications.
• Analysis of overlapping isotopomer envelopes: Disambiguates shared spectral peaks and overlapping isotopomer envelopes in tandem mass spectra.
• Cross-species database matching for unsequenced genomes: Applied to Yersinia rohdei spectra matched against a Yersinia enterocolitica protein database to enable analysis despite an unsequenced genome.

Methodology:

MS-Deconv generates candidate isotopomer envelopes from the input spectrum, converts the spectral data into a graph of envelope nodes and transition edges, scores sets of envelopes, and identifies the highest-scoring subset as a heaviest path.