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Peptide de novo sequencing - mutation detection


Butorac, Ana; Markeš, Marina; Bačun-Družina, Višnja; Cindrić, Mario
Peptide de novo sequencing - mutation detection // Biomolecular Complexes and Assemblies
Primošten, Hrvatska, 2014. (poster, međunarodna recenzija, sažetak, stručni)


Naslov
Peptide de novo sequencing - mutation detection

Autori
Butorac, Ana ; Markeš, Marina ; Bačun-Družina, Višnja ; Cindrić, Mario

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, stručni

Izvornik
Biomolecular Complexes and Assemblies / - , 2014

ISBN
978-953-7941-02-4

Skup
12th Greta Pifat Mruljak International School of Biophysic

Mjesto i datum
Primošten, Hrvatska, 27.9.-6.10.2014

Vrsta sudjelovanja
Poster

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
Peptide de novo sequencing; mutation detection

Sažetak
With the ongoing development of high throughput DNA sequencing technologies and bioinformatics tools, the number of sequenced genomes is exponentially growing. The vast amounts of acquired data are currently available and organized in computer databases[1]. Peptide de novo sequencing presents the analytical process for the reading of amino acid sequences directly from tandem mass spectra (MS/MS). This process is in opposite to “database search” process that matches experimental data against annotated genomes. De novo sequencing is independent from assistance of a sequence database, so it is powerful tool in single mutation determination in organisms with annotated genomes or even in organisms of unknown genomes[2]. In this study we searched for the strain specific mutations by peptide de novo sequencing. We identified particular mutations between Lactobacillus brevis L62 isolated from sourdough and L. brevis ATCC 367 with known genome sequence (National Center for Biotechnology Information, NCBI Accession number NC_008497.1). Furthermore, we used de novo sequencing to determinate mutations between the AmpC enzymes in clinical isolates of Pseudomonas aeruginosa confirming β-lactams antibiotic resistance. For peptide de novo sequencing we used CAF-/CAF+ technique (chemically activated fragmentation negative/chemically activated fragmentation positive)[3]. Acquired peptide sequences are additionally confirmed by Sanger direct DNA sequencing. [1] Lathe W, Williams J, Mangan M, Karolchik D (2008) Genomic Data Resources: Challenges and Promises. Nature Education 1(3):2. [2] Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty‐Kirby A, Lajoie G. (2003) PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid communications in mass spectrometry, 17(20): 2337-2342. [3] Cindrić M, Kraljević PS, Horvatić A, Dodig I. (2014) Mass spectrometry-based protein identification. US 8647880

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Biotehnologija



POVEZANOST RADA


Projekt / tema
058-0583444-3466 - Stresom izazvana raznolikost i evolucija mješovitih bakterijskih kultura (Višnja Bačun-Družina, )

Ustanove
Prehrambeno-biotehnološki fakultet, Zagreb,
Institut "Ruđer Bošković", Zagreb