PROTEOMICS AND METABOLOMICS
PROTEOMICA E METABOLOMICA
| A.Y. | Credits |
|---|---|
| 2024/2025 | 8 |
| Lecturer | Office hours for students | |
|---|---|---|
| Michele Menotta | by appointment on Wednesday 3 to 6 PM. |
| Teaching in foreign languages |
|---|
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Course partially taught in a foreign language
English
This course is taught partially in Italian and partially in a foreign language. Study materials can be provided in the foreign language and the final exam can be taken in the foreign language. |
Assigned to the Degree Course
| Date | Time | Classroom / Location |
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| Date | Time | Classroom / Location |
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Learning Objectives
The aim of the course is to provide knowledge about the proteomics disciplines. Methods and techniques will be exemplified in order to lead the students able to solve proteomics and protein biochemistry problems.
Program
Protein biochemistry. Protein hydrodynamic, amino acid reactivity, post-translational modification (PTM) and reactivity.
Protein extraction methods and sample preparation. Protein extraction methods, protein quantification, cellular and protein fractionation.
Chromatography. Principles, Molecular exclusion chromatography, Hydrophobic interaction chromatography, Reversed-phase chromatography, ion exchange chromatography, affinity chromatography. HPLC, FPLC. Gas chromatography.
Electrophoretic and proteomics. Principles. polyacrylamide gel electrophoresis (PAGE). Native and denaturing PAGE. Isoelectric focusing (IEF). Two-dimensional gel electrophoresis (2D PAGE). Gel staining and analysis. Western Blotting. Spot picking and post-processing.
Mass spectrometry. Introduction to MS. Ionization techniques, MS analyzer. Device coupling and instrumental configurations.
Protein identification. Edman degradation, Tandem MS, CID – Collision induced dissociation. ETD and ECD. Protein sequencing by MS. Peptide Mass Fingerprinting
Bio-informatics tools for protein identification.
Topographic protein distribution. MALDI imaging
PTM analysis methods. Techniques and methods for PTM analysis. Red-ox proteomics
“Gel free” or “shot gun” Proteomics. Quantitative proteomics. Multi-dimensional chromatography. MuDPIT. 18O, SILAC, ICAT, iTRAQ. High-throughput MS based proteomics. DIA e DDA; SWATH-MS e MSe. i High-throughput MS data nalysis.
Proteomics and protein interaction Co-IP, TAP, BioID. Protein Array Analysis. Surface Plasmon Resonance. BRET and FRET. F/D AFM e nano-sensors. Y2H e three-component systems . EMSA. TF array. Chip and Chip-Seq. Membrane extraction. Proximity ligation assay. Complementation assay.
Recombinant proteins and their characterization.
Intro to metabolomics. Metabolites identification: MS/MS, ChemSpider, Predicted compositions. FISh scoring algorithm . quantitative metabolomics, labellingand heavy compounds. Metabolic flux.
Functional networks: Reactome, STRING, PANTHER, DAVID, KEGG. Omic data integration.
Laboratory workshops.
Learning Achievements (Dublin Descriptors)
The student must demonstrate the understanding of the concepts and theories provided by the course. Not only is required the knowledge of the described methods, but also the chemical and physical principles behind the methods (provided during the course). Students have to demonstrate their ability to reason by the discipline logic, and have to independently solve proteomic problems
Teaching Material
The teaching material prepared by the lecturer in addition to recommended textbooks (such as for instance slides, lecture notes, exercises, bibliography) and communications from the lecturer specific to the course can be found inside the Moodle platform › blended.uniurb.it
Teaching, Attendance, Course Books and Assessment
- Teaching
Frontal lessons.
- Attendance
Attendance is strongly suggested
- Course books
- Principles of Proteomics by Richard M. Twyman
- Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis by Josip Lovric
- Introduction to Proteomics: Tools for the New Biology by Daniel C. Liebler
- Principles and Techniques of Practical Biochemistry by Keith Wilson and John Walker
- Clinical Metabolomics- Methods and Protocols”, M. Giera, Humana Press
- Metabolomics: From Fundamentals to Clinical Applications by Alessandra Sussulini
- Assessment
Final oral exam in order to verify whether the student is in line with what is required by the Dublin descriptors
- Disability and Specific Learning Disorders (SLD)
Students who have registered their disability certification or SLD certification with the Inclusion and Right to Study Office can request to use conceptual maps (for keywords) during exams.
To this end, it is necessary to send the maps, two weeks before the exam date, to the course instructor, who will verify their compliance with the university guidelines and may request modifications.
Additional Information for Non-Attending Students
- Teaching
Frontal lessons.
- Attendance
Attendance is strongly suggested
- Course books
“Introduction to Proteomics”, Daniel C. Liebler, Humana Press;
“Clinical Metabolomics- Methods and Protocols”, M. Giera, Humana Press, 2017;
Principles of Proteomics by Richard M. Twyman
Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis by Josip Lovric
Introduction to Proteomics: Tools for the New Biology by Daniel C. Liebler
Principles and Techniques of Practical Biochemistry by Keith Wilson and John Walker
Metabolomics: From Fundamentals to Clinical Applications by Alessandra Sussulini
- Assessment
Oral examination and/or written test.
- Disability and Specific Learning Disorders (SLD)
Students who have registered their disability certification or SLD certification with the Inclusion and Right to Study Office can request to use conceptual maps (for keywords) during exams.
To this end, it is necessary to send the maps, two weeks before the exam date, to the course instructor, who will verify their compliance with the university guidelines and may request modifications.
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