About: CYCLONE-A Utility for De Novo Sequencing of Microbial Cyclic Peptides

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About: CYCLONE-A Utility for De Novo Sequencing of Microbial Cyclic Peptides Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	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. 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. (en)
Title	CYCLONE-A Utility for De Novo Sequencing of Microbial Cyclic Peptides CYCLONE-A Utility for De Novo Sequencing of Microbial Cyclic Peptides (en)
skos:prefLabel	CYCLONE-A Utility for De Novo Sequencing of Microbial Cyclic Peptides CYCLONE-A Utility for De Novo Sequencing of Microbial Cyclic Peptides (en)
skos:notation	RIV/61388971:_____/13:00399080!RIV14-MSM-61388971
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(GAP206/12/1150), P(ME10013)
http://linked.open...iv/cisloPeriodika	8
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Kuzma, Marek Lemr, Karel Kavan, Daniel Havlíček, Vladimír
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Mikrobiologický ústav AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	67619
http://linked.open...ai/riv/idVysledku	RIV/61388971:_____/13:00399080
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	Peptide; Cyclic; Sequencing (en)
http://linked.open.../riv/klicoveSlovo	Cyclic Peptide Sequencing
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[4E7639BF9659]
http://linked.open...i/riv/nazevZdroje	Journal of the American Society for Mass Spectrometry
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Process of ionization during mass spectrometric analysis of small sample amounts. Sampling and efficiency of atmospheric pressure desorption/ionization in mass spectrometric experiment
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	24
http://linked.open...iv/tvurceVysledku	Kavan, Daniel Kuzma, Marek Lemr, Karel Havlíček, Vladimír Schug, K. A.
http://linked.open...ain/vavai/riv/wos	000321923100004
issn	1044-0305
number of pages	8 (xsd:int)
http://bibframe.org/vocab/doi	10.1007/s13361-013-0652-7

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