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Lecturer(s)
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Bílková Zuzana, prof. RNDr. Ph.D.
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Course content
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Introduction, definition of terms, definition of the field of proteomics, connection to other separation and analytical methods. Sample preparation, protein isolation and purification, separation methods used in proteomics. Protein separation using isoelectric focusing. Application of isoelectric focusing as the first dimension of 2D gel electrophoresis. SDS-PAGE for protein separation and its use as a second dimension in 2D gel electrophoresis. Image analysis in gel electrophoresis, processing of individual spots, reagents and enzymes for protein digestion. Proteomic approaches without the use of gel electrophoresis, a multidimensional protein identification technology. Mass spectrometry (MS), principles and possibilities in the analysis of biomolecules (peptides, proteins). Sample preparation for mass spectrometric analysis using MALDI and ESI ionization techniques. Properties of peptides and proteins important for MS analysis. Identification of proteins using tandem MS, de-novo sequencing of peptides, post-translational modification of proteins. Database, software tools and bioinformatic processing of proteomic data. Protein quantification methods. Use of protein and peptide labeling methods. Quantification methods without the use of chemical labeling. Application of proteomic methods and their combinations in practice.
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Learning activities and teaching methods
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Monologic (reading, lecture, briefing), Work with text (with textbook, with book)
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Learning outcomes
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Introduction, definition of terms, definition of the field of proteomics, connection to other separation and analytical methods. Sample preparation, protein isolation and purification, separation methods used in proteomics. Protein separation using isoelectric focusing. Application of isoelectric focusing as the first dimension of 2D gel electrophoresis. SDS-PAGE for protein separation and its use as a second dimension in 2D gel electrophoresis. Image analysis in gel electrophoresis, processing of individual spots, reagents and enzymes for protein digestion. Proteomic approaches without the use of gel electrophoresis, a multidimensional protein identification technology. Mass spectrometry (MS), principles and possibilities in the analysis of biomolecules (peptides, proteins). Sample preparation for mass spectrometric analysis using MALDI and ESI ionization techniques. Properties of peptides and proteins important for MS analysis. Identification of proteins using tandem MS, de-novo sequencing of peptides, post-translational modification of proteins. Database, software tools and bioinformatic processing of proteomic data. Protein quantification methods. Use of protein and peptide labeling methods. Quantification methods without the use of chemical labeling. Application of proteomic methods and their combinations in practice.
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Prerequisites
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unspecified
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Assessment methods and criteria
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Oral examination, Written examination, Home assignment evaluation
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Recommended literature
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Aslam B. et al. Proteomics: Technologies and Their Applications. J. Chromatogr. Sci. 55 (2017) 182-196.
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Figeys D. The basic overview. In: Industrial Proteomics: Applications for Biotechnology and Pharmaceuticals. 2005, John Wiley & Sons, Hoboken.
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Graves P.R., Haystead T.A.J. Molecular Biologist's Guide to Proteomics. Microbiol. Mol. Biol. Rev. 66 (2002) 39-63.
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Maarten Altelaar F. Next-generation proteomics: towards an integrative view of proteome dynamics. Nat. Rev. Genet. 14 (2013) 35-48.
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May C. et al. Instruments and Methods in Proteomics, in: Data Mining in Proteomics. vol. 696, 2010, Humana Press, pp. 3-26.
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Sprenger R.R. et al. Mass Spectrometry Instrumentation in Proteomics. 2012: Wiley online library.
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van Riper S.K. et al. Mass Spectrometry-Based Proteomics: Basic Principles and Emerging Technologies and Directions. Radiation Proteomics, 2013, 1-35.
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Vidová V., Spáčil Z. A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition.. Anal. Chim. Acta 964 (2017) 7-23.
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