CYCLONE—A Utility for De Novo Sequencing of Microbial Cyclic Peptides
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2013
| Date | 2013-08-01 |
| Type | peer-reviewed |
| Venue | Journal of the American Society for Mass Spectrometry |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1007/s13361-013-0652-7 |
| Citations (OpenAlex) | 18 |
| Venue 2-year citedness | 2.84 |
Abstract
We have developed a de novo sequencing software tool (CYCLONE) and applied it for determination of cyclic peptides. The program uses a non-redundant database of 312 nonribosomal building blocks identified to date in bacteria and fungi (more than 230 additional residues in the database list were isobaric). The software was used to fully characterize the tandem mass spectrum of several cyclic peptides and provide sequence tags. The general strategy of the script was based on fragment ion pre-characterization to accomplish unambiguous b-ion series assignments. Showcase examples were a cyclic tetradepsipeptide beauverolide, a cyclic hexadepsipeptide roseotoxin A, a lasso-like hexapeptide pseudacyclin A, and a cyclic undecapeptide cyclosporin A. The extent of ion scrambling in smaller peptides was as low as 5 % of total ion current; this demonstrated the feasibility of CYCLONE de novo sequencing. The robustness of the script was also tested against database sets of various sizes and isotope-containing data. It can be downloaded from the http://ms.biomed.cas.cz/MSTools/ website. ᅟ
Methods and tools
- CYCLONE: A de novo sequencing script for microbial cyclic peptides that assigns b-ion series over a library of 312 nonribosomal building blocks, shown on beauverolide, roseotoxin A, pseudacyclin A and cyclosporin A.
Cites (4)
- A mass spectrometry–guided genome mining approach for natural product peptidogenomics (2011) crossref
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011) crossref
- Dereplication and de novo sequencing of nonribosomal peptides (2009) crossref
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009) crossref
Cited by (3)
- De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments (2020) crossref
- De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments (2019) crossref
- CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra (2015) crossref