DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra
peer-reviewed · Journal of Proteome Research · 2014
peer-reviewed · Journal of Proteome Research · 2014. Thilo Muth et al. De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra…
| Date | 2014-01-07 |
| Type | peer-reviewed |
| Venue | Journal of Proteome Research |
| Publisher | American Chemical Society (ACS) |
| Contribution | adjacent |
| DOI | 10.1021/pr4008078 |
| Citations (OpenAlex) | 83 |
| Venue 2-year citedness | 3.83 |
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.
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- Methodological development in proteomics and lipidomics applied to the analysis of cultural heritage samples : photochemical synthesis of metallic nanoparticles in flow (2026) crossref
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- De Novo Sequencing of Peptides from Tandem Mass Spectra and Applications in Proteogenomics (2024) crossref
- PeposX-Exhaust: A lightweight and efficient tool for identification of short peptides (2024) both
- Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins (2023) both
- Peposx-Exhaust: A Lightweight and Efficient Tool for Identification of Short Peptides (2023) crossref
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- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) both
- Current state, existing challenges, and promising progress for de novo sequencing and assembly of monoclonal antibodies (2022) both
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- DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data (2020) both
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
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- 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
- The sequence coverage in different methods of mass spectrometry data analysis obtained on model proteins (2017) crossref
- Data from proteome analysis of Lasiodiplodia theobromae (Botryosphaeriaceae) (2017) both
- Use of de novo sequencing for proteins identification (2017) crossref
- Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics (2017) crossref
- Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae) (2017) both
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics (2016) crossref
- CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra (2015) crossref
- Venom Proteomics of Indonesian King Cobra, Ophiophagus hannah: Integrating Top-Down and Bottom-Up Approaches (2015) crossref
- Mass spectrometric de novo sequencing of natural non‐tryptic peptides: comparing peculiarities of collision‐induced dissociation (CID) and high energy collision dissociation (HCD) (2014) crossref