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IEEE Computer Society Bioinformatics Conference (CSB'03)
Probability Profiles - Novel Approach in Tandem Mass Spectrometry De Novo Sequencing
Stanford, California
August 11-August 14
ISBN: 0-7695-2000-6
Tema Fridman, Computer Science and Mathematics Division
Robert Day, Computer Science and Mathematics Division
Jane Razumovsbya, Life Sciences Division
Dong Xu, Life Sciences Division
Andrey Gorin, Computer Science and Mathematics Division
A novel method is proposed for deciphering experimental tandem mass spectra. A large database of previously resolved peptide spectra was used to determine "neighborhood patterns" for each peak category: C- or N-terminus ions, their dehydrated fragments, etc. The established patterns are applied to assign probabilities for new spectra peaks to fit into these categories. A few peaks often could be identified with a fair confidence creating strong "anchor points" for De Novo algorithm assembling sequence subgraphs. Our approach is utilizing all informational content of a given MS experimental data set, including peak intensities, weak and noisy peaks, and unusual fragments. We also discuss ways to provide learning features in our method: adjustments for a specific MS device and user initiated changes in the list of considered peak identities.
Citation:
Tema Fridman, Robert Day, Jane Razumovsbya, Dong Xu, Andrey Gorin, "Probability Profiles - Novel Approach in Tandem Mass Spectrometry De Novo Sequencing," csb, pp.415, IEEE Computer Society Bioinformatics Conference (CSB'03), 2003
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