AUDENS: A Tool for Automated Peptide de Novo Sequencing
peer-reviewed · Journal of Proteome Research · 2005
| 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) | 78 |
| Venue 2-year citedness | 3.48 |
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 (2)
Cited by (16)
- PepGo: a deep learning and tree search-based model for de novo peptide sequencing (2025) crossref
- NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics (2024) semanticscholar
- Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023) both
- Denovo-GCN: De Novo Peptide Sequencing by Graph Convolutional Neural Networks (2023) both
- De novo sequencing of proteins by mass spectrometry (2020) both
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Peptide de novo sequencing of mixture tandem mass spectra (2016) both
- UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry (2016) both
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- De Novo Sequencing and Homology Searching (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
- Performance Evaluation of Existing De Novo Sequencing Algorithms (2006) crossref
- Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches (2006) crossref
- Proteomics-Grade de Novo Sequencing Approach (2005) crossref