Differential discovery of protein features using tandem mass spectrometry
| Název práce v češtině: | Diferenční detekce vlastností proteinů pomocí tandemové hmotnostní spektrometrie |
|---|---|
| Název v anglickém jazyce: | Differential discovery of protein features using tandem mass spectrometry |
| Klíčová slova: | protein, hmotnostní spektrometrie, disulfidické můstky, mapování disulfidických můstků, označování fragmentačních spekter |
| Klíčová slova anglicky: | protein, mass spectrometry, disulphide bonds, disulphide bond mapping, fragmentation spectra labelling |
| Akademický rok vypsání: | 2019/2020 |
| Typ práce: | bakalářská práce |
| Jazyk práce: | angličtina |
| Ústav: | Katedra buněčné biologie (31-151) |
| Vedoucí / školitel: | RNDr. Miroslav Kratochvíl, Ph.D. |
| Řešitel: | Bc. Evžen Wybitul - zadáno vedoucím/školitelem, čeká na schválení garantem |
| Datum přihlášení: | 27.05.2020 |
| Datum zadání: | 15.01.2021 |
| Datum odevzdání elektronické podoby: | 12.08.2021 |
| Datum proběhlé obhajoby: | 14.09.2021 |
| Oponenti: | Mgr. Tomáš Pluskal, Ph.D. |
| Seznam odborné literatury |
| - Bauer, Chris, Rainer Cramer, and Johannes Schuchhardt. "Evaluation of peak-picking algorithms for protein mass spectrometry." Data Mining in Proteomics. Humana Press, 2011. 341-352. - Ting, Ying S., et al. "PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data." Nature methods 14.9 (2017): 903. - Henning, Jessica, Annika Tostengard, and Rob Smith. "A Peptide-Level Fully Annotated Data Set for Quantitative Evaluation of Precursor-Aware Mass Spectrometry Data Processing Algorithms." Journal of proteome research 18.1 (2018): 392-398. - Tyanova, Stefka, Tikira Temu, and Juergen Cox. "The MaxQuant computational platform for mass spectrometry-based shotgun proteomics." Nature protocols 11.12 (2016): 2301. - Matthiesen, Rune, ed. Mass spectrometry data analysis in proteomics. Vol. 367. Totowa, NJ: Humana Press, 2007. |
| Předběžná náplň práce |
| Cílem práce je shrnout poznatky o využití tandemové hmotnostní spektroskopie pro studium struktury proteinů. |
| Předběžná náplň práce v anglickém jazyce |
| Mass spectrometry has become an indisposable tool for identification of various chemicals, ranging in size from single isotopes and small molecules to large protein complexes. In particular, spectra obtained from tandem mass spectrometry provide information about the precise mass of the sample and m/z values of its fragments, which gives a natural possibility to reconstruct even very large chemical structures. Because the naive matching of the spectra to the vast space of chemical structures is computationally hard, practical methods usually incorporate various heuristics and prior information about the sample, which simplify the analysis. This thesis will review the currently available strategies and heuristics used for the identification. The results will be used to construct a custom variant of the identification algorithm useful for identifying presence of specific chemical features on proteins (e.g. disulfide bonds) by differential analysis under various peptide modifications, including the targeted modifications (alkylation, enzymatic cleveage, disulfide bond modifications) and the ones occurring spontaneously during the measurement (oxidation, deamination). Performance (computation speed and precision) of the algorithm will be evaluated on locally generated datasets. |