CYCLONE--a utility for de novo sequencing of microbial cyclic peptides
Language English Country United States Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- Bacteria chemistry MeSH
- Peptides, Cyclic chemistry MeSH
- Cyclosporine chemistry MeSH
- Databases, Genetic MeSH
- Databases, Protein MeSH
- Depsipeptides chemistry MeSH
- Gene Library MeSH
- Fungi chemistry MeSH
- Reference Standards MeSH
- Solvents MeSH
- Data Collection MeSH
- Amino Acid Sequence MeSH
- Sequence Analysis, Protein methods MeSH
- Software MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- beauverolides MeSH Browser
- Peptides, Cyclic MeSH
- Cyclosporine MeSH
- Depsipeptides MeSH
- Solvents MeSH
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
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CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra
