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CycloBranch - The stand-alone and open-source de novo peptide identification engine

Events

16. November 2017
10:00-11:30

: Anna-Spiegel Translational Research Center, Spitalgasse 23, 1090 Vienna, Seminar room, 3. Floor

Event zum Kalender hinzufügen (ICAL)

Dr. Jiri Novak
Postdoctoral researcher, scientific software developer and bioinformatician at the Institute of Microbiology of the Czech Academy of Sciences, Prague.

Host: Goran Mitulović


Dr. Jiri Novak is a postdoctoral researcher, scientific software developer and bioinformatician at the Institute of Microbiology of the Czech Academy of Sciences.
He received his Ph.D. degree in Software Systems at the Faculty of Mathematics and Physics of the Charles University in Prague for his dissertation “Similarity Search in Mass Spectra Databases” in 2013 and M.S. degree in Computer Science at the Faculty of Electrical Engineering of the Czech Technical University in Prague in 2009.
In 2012, Dr. Novak was awarded by FEBS Short-Term Fellowship and spent a 3 months research stay focused on computational mass spectrometry in Applied Bioinformatics Group at Eberhard-Karls-Universität Tübingen, Germany.
Dr. Novak is interested in the development of computational methods and software tools for automated processing of high-resolution mass spectrometry data.
E-mail: jiri.novak@biomed.cas.cz
Web: ms.biomed.cas.cz/staff-novak_jiri.php
ResearcherID: J-8071-2014

The stand-alone and open-source de novo peptide identification engine CycloBranch was effectively utilized for identification or sequence tag determination of NRPs from accurate product ion mass spectra. It represents the first and true de novo engine working for nonribosomal peptides. It supports sequencing of linear, branched, and branch-cyclic NRPs as well as cyclic peptides. NRP sequence tags were provided in the output even when a building block was not present in a database or the spectrum contained incomplete fragment ion series. The parts of an unknown structure, if not covered by database building blocks or their combinations, are returned as exact monoisotopic masses in suggested sequence tags.


References:
1: Novák J, Sokolová L, Lemr K, Pluháček T, Palyzová A, Havlíček V.
Batch-processing of imaging or liquid-chromatography mass spectrometry datasets and De Novo sequencing of polyketide siderophores. Biochim Biophys Acta. 2017 Jul;1865(7):768-775. doi: 10.1016/j.bbapap.2016.12.003. Epub 2016 Dec 9. PubMed PMID: 27956353.
2: Novák J, Lemr K, Schug KA, Havlíček V. CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra. J Am Soc Mass Spectrom. 2015 Oct;26(10):1780-6. doi: 10.1007/s13361-015-1211-1. Epub 2015 Jul 21. PubMed PMID: 26195308.