Mass Spectrometry applied to Proteomics
Objectives
1. Understand the importance of mass spectrometry in revealing how biological processes work at the cellular and molecular levels
2. Understand the use of mass spectrometry to study protein dynamics in complex biological systems
3. Apply the chemistry underpinning the biological processes
4. Apply the chemistry underpinning the techniques used in proteomics
5. Experimental design and sample preparation for mass spectrometry analysis
6. Understand proteomics to such an extent that the student will be able to utilize proteomics core facilities.
7. Demonstrate how modern proteomics is applied to different fields (i.e. Medicine, Biology, Biotechnology, Environmental Sciences).
General characterization
Code
12411
Credits
3.0
Responsible teacher
Hugo Miguel Baptista Carreira dos Santos, José Luís Capelo Martinez
Hours
Weekly - 2
Total - 35
Teaching language
Português
Prerequisites
Knowledge in General Biochemistry.
A laptop is advised.
Bibliography
[1] Modern proteomics – Sample preparation, Analysis and Practical Applications. Hamid Mirzaei, Martin Carrasco. Springer, 2016.
[2] Quantitative Proteomics by Mass Spectrometry. Second edition. Springer protocols. Salvatore Sechi, 2018.
[3] Proteome Bioinformatics. Springer protocols. Shivakumar Keerthikumar and Suresh Mathivanan, 2018
[4] Identifying microbes by mass spectrometry proteomics. Charles H. Wick. CRC Press. 2013.
Teaching method
Students will learn basics and advanced concepts of mass spectrometry and their application to (i) Identification of microorganisms; (ii) Biomarker discovery in biomedicine; (iii) Pharmaceutical proteomics; (iv) Single cell proteomics, (v) Environmental proteomics e (vi) Analysis of post-translational modification by mass spectrometry. The software learnt address the student to deal with large series of proteomics data to identify
Evaluation method
The course will have both theoretical and laboratory classes. Laboratory work (mostly with computer) will be developed by the students under teacher supervision. Evaluation includes In-class short-answer papers – 5 % of total mark; problem sheets – 10 % of total mark Lab-work; – 25 % of total mark; individual proteomics project – 30 % of total mark; examination – 30 % of total mark
Subject matter
1. Introduction to proteomics
2. Supramolecular separations
2.1 Protein separation
2.2 two-dimensional gel electrophoresis
2.3 liquid-chromatography
3. Fundamentals of MS
3.1 Mass spectrometry in proteomics
3.2 Ionization techniques (MALDI and ESI)
3.3 Mass analyzers
3.4 Tandem MS in space
3.5 Tandem time MS/MS
4. Quantitative MS
4.1 Protein quantification.
4.2 Relative and absolute quantification
4.3 Stable isotope labeling in mass spectrometry
4.4 Label-free quantitative mass spectrometry
5. Protein databases and bioinformatics
6. Experimental design and quality control
7. Applications
7.1 Identification of microorganisms
7.2 Biomarkers in biomedicine
7.3 Pharmaceutical proteomics
7.4 Single-cell proteomics
7.5 Environmental proteomics