DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra
peer-reviewed · Journal of Proteome Research · 2014
| Date | 2014-01-07 |
| Type | peer-reviewed |
| Venue | Journal of Proteome Research |
| Publisher | American Chemical Society |
| Contribution | adjacent |
| DOI | 10.1021/pr4008078 |
| Citations (OpenAlex) | 89 |
| Venue 2-year citedness | 3.48 |
Abstract
De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .
Methods and tools
- DeNovoGUI: Open-source Java graphical user interface for tandem-MS de novo sequencing. Wraps PepNovo+, DirecTag, Novor, and pNovo behind a single workflow with shared input/output handling and result inspection. From the CompOmics group at Ghent + collaborators in Bergen, Magdeburg, and Salzburg.
Cites (4)
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) both
- Performance Evaluation of Existing De Novo Sequencing Algorithms (2006) both
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
Cited by (13)
- CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo (2026) both
- Learning Fragmentation Physics or Exploiting Sequence Priors? Benchmarking Bias in Deep Learning Models for De Novo Peptide Sequencing (2026) crossref
- DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics (2026) crossref
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) both
- Venomics and antivenomics of Indian spectacled cobra (Naja naja) from the Western Ghats (2022) crossref
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
- Extended Snake Venomics by Top-Down In-Source Decay: Investigating the Newly Discovered Anatolian Meadow Viper Subspecies, Vipera anatolica senliki (2020) both
- Delineating the venom toxin arsenal of Malabar pit viper (Trimeresurus malabaricus) from the Western Ghats of India and evaluating its immunological cross-reactivity and in vitro cytotoxicity (2020) crossref
- Postnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing (2018) crossref
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- Mass spectrometry-assisted venom profiling of Hypnale hypnale found in the Western Ghats of India incorporating de novo sequencing approaches (2018) crossref
- Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics (2017) crossref
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref