AUDENS: A Tool for Automated Peptide de Novo Sequencing
peer-reviewed · Journal of Proteome Research · 2005
peer-reviewed · Journal of Proteome Research · 2005. Jonas Grossmann et al. We present AUDENS, a new platform-independent open source tool for automated de novo sequencing of peptides…
| Date | 2005-10-01 |
| Type | peer-reviewed |
| Venue | Journal of Proteome Research |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1021/pr050070a |
| Citations (OpenAlex) | 79 |
| Venue 2-year citedness | 3.83 |
Preprint version: AuDeNS: A tool for automatic De Novo peptide sequencing (2002-01-01, Repository for Publications and Research Data (ETH Zurich))
Abstract
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 http://www.ti.inf.ethz.ch/pw/software/audens/ .
Methods and tools
- AUDENS: Open-source automated de novo sequencing tool with preprocessing and dynamic programming over MS/MS spectra.
Cites (3)
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by Fourier transform ion cyclotron resonance mass spectrometry (2004) crossref
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