CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2015
| Date | 2015-10-01 |
| Type | peer-reviewed |
| Venue | Journal of the American Society for Mass Spectrometry |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1007/s13361-015-1211-1 |
| Citations (OpenAlex) | 45 |
| Venue 2-year citedness | 2.84 |
Abstract
Nonribosomal peptides have a wide range of biological and medical applications. Their identification by tandem mass spectrometry remains a challenging task. A new open-source de novo peptide identification engine CycloBranch was developed and successfully applied in identification or detailed characterization of 11 linear, cyclic, branched, and branch-cyclic peptides. CycloBranch is based on annotated building block databases the size of which is defined by the user according to ribosomal or nonribosomal peptide origin. The current number of involved nonisobaric and isobaric building blocks is 287 and 521, respectively. Contrary to all other peptide sequencing tools utilizing either peptide libraries or peptide fragment libraries, CycloBranch represents a true de novo sequencing engine developed for accurate mass spectrometric data. It is a stand-alone and cross-platform application with a graphical and user-friendly interface; it supports mzML, mzXML, mgf, txt, and baf file formats and can be run in parallel on multiple threads. It can be downloaded for free from http://ms.biomed.cas.cz/cyclobranch/ , where the User’s manual and video tutorials can be found.
Methods and tools
- CycloBranch: Open-source de novo identification engine for nonribosomal peptides, reading accurate product ion masses to handle linear, cyclic and branched topologies that ordinary peptide tools cannot express.
Cites (9)
- DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra (2014) crossref
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Dereplication and de novo sequencing of nonribosomal peptides (2009) crossref
- Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides (2007) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) crossref
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) crossref