ADEPTS: advanced peptide de novo sequencing with a pair of tandem mass spectra

J Bioinform Comput Biol. 2010 Dec;8(6):981-94. doi: 10.1142/s0219720010005099.


De novo sequencing is an important task in proteomics to identify novel peptide sequences. Traditionally, only one MS/MS spectrum is used for the sequencing of a peptide; however, the use of multiple spectra of the same peptide with different types of fragmentation has the potential to significantly increase the accuracy and practicality of de novo sequencing. Research into the use of multiple spectra is in a nascent stage. We propose a general framework to combine the two different types of MS/MS data. Experiments demonstrate that our method significantly improves the de novo sequencing of existing software.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Artificial Intelligence
  • Computational Biology
  • Databases, Protein / statistics & numerical data
  • Likelihood Functions
  • Peptides / chemistry*
  • Peptides / genetics
  • Sequence Analysis, Protein / statistics & numerical data*
  • Software
  • Tandem Mass Spectrometry / statistics & numerical data*


  • Peptides