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
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