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Contact: Xiaowen Liu [liuxiaowencs (at)]


Top-down proteomics studies intact proteins, enabling new opportunities for analyzing post-translational modifications. Because tandem mass spectra of intact proteins are very complex, spectral deconvolution (grouping peaks into isotopomer envelopes) is a key initial stage for their interpretation. In such spectra, isotopomer envelopes of different protein fragments span overlapping regions on the m/z axis and even share spectral peaks. This raises both pattern recognition and combinatorial challenges for spectral deconvolution. 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 a heaviest path in the graph. In contrast with other approaches, the algorithm scores sets of envelopes rather than individual envelopes.






Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.
Xiaowen Liu, Yuval Inbar, Pieter C. Dorrestein, Colin Wynne, Nathan Edwards, Puneet Souda, Julian P. Whitelegge, Vineet Bafna and Pavel A. Pevzner.
Molecular and Cellular Proteomics, 9:2772-2782, 2010.

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