Università degli Studi di Urbino Carlo Bo / Portale Web di Ateneo


PROTEOMICS
PROTEOMICA

A.Y. Credits
2018/2019 8
Lecturer Email Office hours for students
Michele Menotta by appointment on Wednesday 3 to 6 PM.
Teaching in foreign languages
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

Sanitary Nutritional and Environmental Biology (LM-6)
Curriculum: BIOTECNOLOGIE MOLECOLARI
Date Time Classroom / Location
Date Time Classroom / Location

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. 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.

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 proteomics 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 
  • 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.

    Additional Information for Non-Attending Students

    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.

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