Iščitavanje reverzne translacije sekvenciranjem peptida de novo tehnikama tandemne spektrometrije masa

Dodig, Ivana

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doctoral thesis

Iščitavanje reverzne translacije sekvenciranjem peptida de novo tehnikama tandemne spektrometrije masa

Zagreb: University of Zagreb, Faculty of Science, 2016. urn:nbn:hr:217:611174

Dodig, Ivana

University of Zagreb
Faculty of Science
Department of Chemistry

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APA 6th Edition

Dodig, I. (2016). Iščitavanje reverzne translacije sekvenciranjem peptida de novo tehnikama tandemne spektrometrije masa (Doctoral thesis). Retrieved from https://urn.nsk.hr/urn:nbn:hr:217:611174

MLA 8th Edition

Dodig, Ivana. "Iščitavanje reverzne translacije sekvenciranjem peptida de novo tehnikama tandemne spektrometrije masa." Doctoral thesis, University of Zagreb, Faculty of Science, 2016. https://urn.nsk.hr/urn:nbn:hr:217:611174

Chicago 17th Edition

Harvard

Dodig, I. (2016). 'Iščitavanje reverzne translacije sekvenciranjem peptida de novo tehnikama tandemne spektrometrije masa', Doctoral thesis, University of Zagreb, Faculty of Science, accessed 26 March 2023, https://urn.nsk.hr/urn:nbn:hr:217:611174

Vancouver

Dodig I. Iščitavanje reverzne translacije sekvenciranjem peptida de novo tehnikama tandemne spektrometrije masa [Doctoral thesis]. Zagreb: University of Zagreb, Faculty of Science; 2016 [cited 2023 March 26] Available at: https://urn.nsk.hr/urn:nbn:hr:217:611174

IEEE

I. Dodig, "Iščitavanje reverzne translacije sekvenciranjem peptida de novo tehnikama tandemne spektrometrije masa", Doctoral thesis, University of Zagreb, Faculty of Science, Zagreb, 2016. Available at: https://urn.nsk.hr/urn:nbn:hr:217:611174

Cite this item: https://urn.nsk.hr/urn:nbn:hr:217:611174

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Title	Iščitavanje reverzne translacije sekvenciranjem peptida de novo tehnikama tandemne spektrometrije masa
Title (english)	Scanning of reverse translation via de novo peptide sequencig by tandem mass spectrometry
Author	Ivana Dodig
Mentor	Mario Cindrić (mentor)
Committee member	Ita Gruić Sovulj (predsjednik povjerenstva)
Committee member	Mario Cindrić (član povjerenstva)
Committee member	Predrag Novak (član povjerenstva)
Granter	University of Zagreb Faculty of Science (Department of Chemistry) Zagreb
Defense date and country	2016-07-22, Croatia
Scientific / art field, discipline and subdiscipline	NATURAL SCIENCES Chemistry
Universal decimal classification (UDC)	54 - Chemistry. Crystallography. Mineralogy
Abstract	Sekvenciranje peptida i proteina de novo korišteno je kao alat za reverzno iščitavanje translacije. Pri tome je nedvojbeno sekvenciranje de novo omoguceno selektivnim obilježavanjem N-kraja peptida 5-formil-1,3-benzen-di-sulfonicnom kiselinom prije analize tandemnom spektrometrijom masa. Opisana kemijska modifikacija usmjerava fragmentaciju peptidnih iona ka disocijaciji peptidne veze prilikom kolizijom inducirane disocijacije u spektrometru masa. Nastali fragmentni ioni b-serije detektiraju se u negativnom načinu rada spektrometra masa, a fragmentni ioni y-serije detektiraju se u pozitivnom načinu spektrometra masa. Stoga je, za isti peptid, aminokiselinski slijed iščitan iz spektra snimljenog u pozitivnom načinu rada spektrometra masa moguće dodatno provjeriti iščitavanjem iz spektra snimljenog pri negativnom načinu rada spektrometra masa (tzv. nedvojbeno sekvenciranje peptida de novo). Jedna od primjena ovakvog načina sekvenciranja de novo je i identifikacija proteina, koja se provodi pretragom, iz spektra iščitane sekvence peptida, u bazi podataka, odnosno iščitavanjem reverzne translacije. Disertacija prikazuje primjenjivost, pouzdanost i točnost kao i komparativnu prednost novorazvijene de novo tehnike nad klasičnim tehnikama identifikacije proteina.
Abstract (english)	De novo peptide and protein sequencing was used as a tool for reverse translation scanning. Unambiguous de novo sequencing is achived by selective derivatization of peptide N-terminus by 5-formyl-1,3-benzendisulfonic acid before tandem mass spectrometry analysis. Described chemical modification of peptide directs fragmentation pathway to the peptide bound dissociation during collision-induced dissociation in the mass spectrometer. The resulting b-series of fragmentation ions is detected in the negative ion mode of the mass spectrometer, and y-series of fragmentation ions is detected in the positive ione mode of the mass spectrometer. Therefore, for the same peptide, amino acid sequence read out from the spectrum recorded in the positive ione mode can be additionally verified by reading out from the spectrum obtained in the negative ion mode of mass spectrometer (the so-called unambiguous de novo sequencing). One application of the described de novo sequencing technique is protein identification, which is performed by searching for previously spectral obtained peptide sequence, in the protein database ie. by scanning of reverse translation. This thesis presents applicability, reliability and accuracy as well as the comparative advantage of the newly developed de novo sequencing technique over the conventional protein identification techniques.
Keywords
Keywords (english)
Language	croatian
URN:NBN	urn:nbn:hr:217:611174
Study programme	Title: Doctoral study in chemistry Study programme type: university Study level: postgraduate Academic / professional title: doktor/doktorica znanosti, područje prirodnih znanosti, polje kemija (doktor/doktorica znanosti, područje prirodnih znanosti, polje kemija)
Type of resource	Text
Extent	191 str. ; 30 cm
File origin	Born digital
Access conditions	Open access
Terms of use
Repository	Repository of the Faculty of Science
Created on	2017-03-09 10:23:08