מבוא לחלבונאות (0421.3381)
Introduction to Proteomics
Introduction to proteomics will cover all major fields of the modern proteomics. It will give comprehensive information about theoretical basics of proteomics, different methods and approaches. The course will cover techniques of protein and peptide preparation for mass-spectrometry analysis, separation and enrichment methods, theoretical knowledge about different types of mass-spectrometry used in proteomic research, approaches of quantitative proteomics and detection of post-translational modifications, top-down and structural proteomics. Finally, information will be provided regarding use of mass-spectrometry for tissue imaging. By the end of the course the students will be able to understand manuscripts describing proteomic data, also they will be able to read and interpret spectra, detect post-translational modifications, to know major protocols used in proteomic analysis, to design biological experiments for quantitative proteomics study.

List of topics
1. Introduction to Proteomics: Proteome, field of research, tools to study proteome. Categories of proteomics
2. Introduction to Peptide/Protein separations techniques (given by Prof. G. Fleminger)
a. Electrophoresis: Blue native gels, SDS gels: 1D and 2D, 2D DIGE. Protein detection
b. Liquid chromatography
i. Definitions, theory of liquid chromatography
ii. Affinity chromatography
iii. Gel Filtration
iv. Reverse phase chromatography
v. Strong cation exchange chromatography
vi. High pH anion exchange chromatography
vii. Multidimensional HPLC
viii. Devices
c. Capillary electrophoresis
3. Preparation of proteins and peptides for mass spectrometry:
a. Denaturation
b. Reduction
c. Alkylation
d. Digestion and digestion enzymes, types of products
i. In-gel digestion
ii. In-solution digestion
4. Mass-Spectrometry: Ionization
a. Ionization techniques overview
b. MALDI
c. ESI, microESI, nanoESI
5. Mass-Spectrometry: fragmentation
a. CID
b. ECD
c. ETD
d. IRD
6. Mass-Spectrometry: analyzers
a. TOF
b. Quadrupole
c. Ion trap
d. FT-ICR
e. Orbitrap
7. Mass-Spectrometry: detectors and data acquisition
8. Tandem mass-spectrometers
9. Mass Spectra: interpretation:
a. Database search
b. De novo analysis
c. Manual verification
d. Software
10. Ion mobility spectroscopy
11. Quantitative proteomics (absolute and relative)
a. Label-free quantitation
i. Spectral counting ratio
ii. Spectral TIC ratio
iii. MSE based quantitation
b. Labeled:
i. AQUA
ii. ICAT
iii. iTRAQ and TMT
iv. SILAC and modifications
c. Statistical analysis of quantitative proteomic data
12. Post-translational modifications: phosphorylation
a. Enrichment
b. Detection
c. Differential interpretation
i. Difference from sulfation
d. Techniques used for phosphorylation detection
13. Post-translational modification: Glycosylation
a. O-glycosylation
b. N-glycosylation
14. Other PTMs:
a. Acetylation
b. Methylation
c. Ubiquitination
15. Reproducibility of Mass-spectrometry data, Validation
a. MS-based validation: SRM/MRM transitions
b. Non-mass-spec based validation
16. Top-down proteomics
17. Mass-spectrometry of protein conformation, protein-protein interactions
a. Mass-Spectrometry of proteins and protein complexes
b. Ion mobility spectroscopy
c. H/D exchange mass-spectrometry
d. Use of ETD
18. Non-mass-spectrometry based proteomics (given by Dr. E. Perlson)
a. Protein chips
19. Imaging mass-spectrometry
דרישות קדם: Advanced level of knowledge in biochemistry, organic chemistry, physics and statistics is required.
Course 0453.3391: Separation Processes for Biological Products, is highly recommended
נוכחות חובה
הרכב ציון:
Evaluation will be based on multiple-choice exam (50 questions).
מטלת סיום: בחינה בכתב