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.

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.

Proteomics and protein interaction Co-IP, TAP. 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.

Functional networks.

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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 proteomics problems

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

n/a

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 

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.

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

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.