title: CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra.
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.
authors.affiliation: Institute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech Republic. jiri.novak@biomed.cas.cz.
authors.forename: Jiří
authors.initials: J
authors.lastname: Novák
authors.affiliation: Institute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech Republic.|Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic.
authors.forename: Karel
authors.initials: K
authors.lastname: Lemr
authors.affiliation: Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019-0065, USA.
authors.forename: Kevin A
authors.initials: KA
authors.lastname: Schug
authors.affiliation: Institute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech Republic. vlhavlic@biomed.cas.cz.|Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic. vlhavlic@biomed.cas.cz.
authors.forename: Vladimír
authors.initials: V
authors.lastname: Havlíček
mesh_terms: D000465:Algorithms; D010446:Peptide Fragments; D010455:Peptides / Q000032:analysis* / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D010446:Peptide Fragments; D010455:Peptides
keywords: Branch-cyclic; Branched; Cyclic; De novo sequencing; Linear; Nonribosomal peptides