AUDENS: a tool for automated peptide de novo sequencing

J Proteome Res. Sep-Oct 2005;4(5):1768-74. doi: 10.1021/pr050070a.


We present AUDENS, a new platform-independent open source tool for automated de novo sequencing of peptides from MS/MS data. We implemented a dynamic programming algorithm and combined it with a flexible preprocessing module which is designed to distinguish between signal and other peaks. By applying a user-defined set of heuristics, AUDENS screens through the spectrum and assigns high relevance values to putative signal peaks. The algorithm constructs a sequence path through the MS/MS spectrum using the peak relevances to score each suggested sequence path, i.e., the corresponding amino acid sequence. At present, we consider AUDENS a prototype that unfolds its biggest potential if used in parallel with other de novo sequencing tools. AUDENS is available open source and can be downloaded with further documentation at .

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Arabidopsis / metabolism
  • Complement System Proteins
  • Internet
  • Ions
  • Mass Spectrometry
  • Molecular Sequence Data
  • Peptides / chemistry
  • Plant Proteins / chemistry
  • Sensitivity and Specificity
  • Sequence Analysis, Protein / instrumentation*
  • Sequence Analysis, Protein / methods*
  • Software*


  • Ions
  • Peptides
  • Plant Proteins
  • Complement System Proteins