CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass SpectraClick to copy article linkArticle link copied!
- Jiří NovákJiří NovákInstitute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech RepublicMore by Jiří Novák
- Karel LemrKarel LemrInstitute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech RepublicRegional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech RepublicMore by Karel Lemr
- Kevin A. SchugKevin A. SchugDepartment of Chemistry and Biochemistry, The University of Texas at Arlington, 76019-0065, Arlington, TX, USAMore by Kevin A. Schug
- Vladimír HavlíčekVladimír HavlíčekInstitute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech RepublicRegional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech RepublicMore by Vladimír Havlíček
Abstract
![Abstract Image](/cms/10.1007/s13361-015-1211-1/asset/images/medium/js8b04900_0006.gif)
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.
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