Recent Developments in Computational Methods for De Novo Peptide Sequencing from Tandem Mass Spectrometry (MS/MS)

Author(s): Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu.

Journal Name: Protein & Peptide Letters

Volume 22 , Issue 11 , 2015

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Abstract:

Tandem mass spectrometry (MS/MS) has emerged as a major technology for peptide sequencing. Typically, there are three kinds of methods for the peptide sequencing: database searching, peptide tagging, and de novo sequencing. De novo sequencing has drawn increasing attention because of its independence from existing protein databases and potential for identifying new proteins, proteins resulting from mutations, proteins with unexpected modifications and so on. Recently, with the improvements in the accuracy of MS/MS and development of alternative fragmentation modes of MS/MS, many new de novo sequencing methods have been formulated. This paper reviews these recently developed sequencing methods including those for alternative MS/MS spectra. The paper first introduces background knowledge on peptide sequencing and mass spectrometry, and then reviews de novo peptide sequencing methods for traditional CID spectra. After that, it focuses on the recent development of de novo methods for alternative MS/MS spectra. In addition, methods using multiple spectra from the same peptide are surveyed. Finally, conclusions and some directions of future work are discussed.

Keywords: De novo peptide sequencing, fragmentation techniques, graph theoretical model, multiple spectra, proteomics, tandem mass spectrometry.

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Article Details

VOLUME: 22
ISSUE: 11
Year: 2015
Page: [983 - 991]
Pages: 9
DOI: 10.2174/0929866522666150821113127
Price: $65

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