MS-Deconv

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Contact: Xiaowen Liu [liuxiaowencs (at) gmail.com]

Summary

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.

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MS-Deconv 0.8.0.7370

Publication

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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MS-Deconv

0.8.0.7370

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