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Lecturer(s)
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Šebela Marek, prof. Mgr. Dr.
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Course content
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1) Spectrophotometric quantification of proteins (Bradford, BCA, UV absorption) 2) Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS-PAGE) 3) Isoelectric focusing in a polyacrylamide gel 4) Gel scanning, image analysis (software LabScan and GelAnalyzer) 5) Spot excision, sample reduction and alkylation process, proteolytic cleavage of sample in gel and in solution 6) Desalting of protein and peptide samples, peptide mapping on a MALDI-TOF mass spectrometer (software mMass and Mascot), computer prediction of protein cleavage (software Protein Cutter and Peptide Mass) 7) Measurement of tandem mass spectra of peptides on a MALDI-TOF/TOF spectrometer, data evaluation 8) De novo protein sequencing on a MALDI-TOF/TOF spectrometer, data evaluation 9) nLC-MALDI MS/MS analysis of a complex protein sample, data evaluation 10) Measurement of MALDI-TOF protein profiles of intact microorganisms, data evaluation (dendrograms) 8) Measuring tandem mass spectra of peptides and glycopeptides using a MALDI-TOF/TOF instrument 9) nLC-MALDI MS/MS analysis of a complex protein sample 10) Measuring MALDI-TOF protein profiles of intact microorganisms, working with the program Biospean
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Learning activities and teaching methods
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Dialogic Lecture (Discussion, Dialog, Brainstorming), Laboratory Work, Group work
- Attendace
- 78 hours per semester
- Homework for Teaching
- 100 hours per semester
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Learning outcomes
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Students perform hands-on experiments to learn how to apply basic analysis plus separation and instrumental methods used in proteomics.
Students learn to apply and practice basic proteomic procedures and methods.
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Prerequisites
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Knowledge and skills acquired through successful completion of the KBC/BCH Fundamentals of Biochemistry, or KBC/UBC(H) Introduction to Biochemistry, or KBC/ZBINF(ZBINU) Fundamentals of Bioinformatics are required. The course also practically develops knowledge from KBC/PROT Proteomics and KBC/BIME Biochemical methods.
KBC/PROT
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Assessment methods and criteria
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Student performance, Analysis of Activities ( Technical works), Systematic Observation of Student
Successful completion of assigned laboratory tasks, data processing and submission of the relevant reports.
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Recommended literature
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Link, A.J.; LaBaer, J. (2009). Proteomics: A Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor, USA.
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Link, Andrew J., LaBaer, Joshua. (2009). Proteomics. A Cold Spring Harbor Laboratory Course Manual. CSH Press, Cold Spring Harbor, New York.
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Mirzaei, H.; Carrasco, M. (Eds.). (2016). Modern Proteomics: Sample Preparation, Analysis and Practical Applications. Cham, Switzerland.
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