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

peer-reviewed · Protein & Peptide Letters · 2015

peer-reviewed · Protein & Peptide Letters · 2015. Yan Yan et al. Tandem mass spectrometry (MS/MS) has emerged as a major technology for peptide sequencing. Typically, there…
Date 2015-09-23
Type peer-reviewed
Venue Protein & Peptide Letters
Publisher Bentham Science Publishers Ltd.
Contribution review
DOI 10.2174/0929866522666150821113127
Citations (OpenAlex) 7
Venue 2-year citedness 3.13

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.

Authors

  1. Yan Yan · University of Saskatchewan, University of Western Ontario
  2. Anthony J. Kusalik · University of Saskatchewan
  3. Fang-Xiang Wu · University of Saskatchewan

Methods and tools

Cited by (3)

Seen in the charts

Back to the full map

Back to top