Određivanje mikroorganizama pomoću MS/MS analize proteoma

master's thesis

• Title (english): Microbial detection and identification using mass spectrometry proteome analysis
• Author: Sara Ujević
• Mentor: Antonio Starčević (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2016-09-26, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

„Shotgun” tehnika u proteomici postala je široko primjenjiva. Zasniva se na digestiji proteina, sekvenciranju dobivenih peptida tandemnom spektrometrijom masa nakon čega slijedi identifikacija proteina pretragom baze podataka. Tehnike tandemne spektrometrije masa postaju sve privlačnije za identifikaciju mikroorganizama zahvaljujući njihovoj brzini i niskoj cijeni. Razvojem tehnološki naprednijih uređaja za spektrometriju masa postignuta je veća preciznost mjerenja čime se povećala količina dobivenih podataka. Unatoč tome, bioinformatička analiza tih podataka i dalje predstavlja veliki problem zbog nedostatka prikladnih bioinformatičkih alata. U ovom radu uspoređeni su bioinformatički alati, ProteinLynx Global Server (PLGS) i novorazvijeni alat koji se zasniva na LSI metodi, s ciljem određivanja vrste odnosno soja mikroorganizma. Rezultati su pokazali da je novorazvijeni bioinformatički alat daleko učinkovitiji te za razliku od PLGS-a ne zahtijeva sužavanje područja pretrage i ne ovisi u tolikoj mjeri o preciznosti snimanja samog uređaja. Ovim alatom uspješno je određen analizirani soj kvasca Candida albicans SC5314.

Abstract (english)

The shotgun proteomics strategy has become widely adopted. It is based on digesting proteins into peptides followed by peptide sequencing using tandem mass spectrometry (MS/MS) and automated database searching. Tandem mass spectrometry methods are becoming increasingly attractive for identifying microorganisms, mainly due to their speed and low cost. Drastic improvements in accuracy of mass spectrometry devices have led to an increasment of data being generated. Nevertheless, structuring such information is still hard due to lack of appropriate bioinformatics tools. In this work two bioinformatics tools, ProteinLynx Global Server (PLGS) and novel bioinformatic algorithm based on LSI, have been compared in order to identify microbial species i.e. strains. Unlike PLGS, the results showed that this novel algorithm proved to be more efficient because it is not limited by database search area and also not constrained by accuracy of the mass spectrometry devices. Candida albicans SC5314 has been successfully detected and identified by this novel algorithm.

• Keywords: proteomika; digestija; tandemna spektrometrija masa; bioinformatički algoritam; LSI
• Keywords (english): proteomics; digestion; tandem mass spectrometry; bioinformatic algorithm; LSI
• Language: croatian
• URN:NBN: urn:nbn:hr:159:992242
• Study programme: Title: Molecular Biotechnology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka molekularne biotehnologije (magistar/magistra inženjer/inženjerka molekularne biotehnologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2017-04-25 08:20:16