CHIMICA DELLE PROTEINE E PROTEOMICA

The aim of the course is to provide students with the most recent and updated basic knowledge in the field of protein chemistry and proteome analysis. Particularly, this knowledge will be useful to address the characterization of complex protein mixtures via proteomic approaches, involving the use of electrophoretic and chromatographic techniques, protein enzymatic digestion (in-gel and in solution), mass spectrometry analysis and, bioinformatics tools.

Furthermore, in reference to the so-called Dublin Descriptors, this course helps to acquire the following skills:

D1 - Knowledge and understanding: The students will have to demonstrate their basic knowledge related to the analytical methods used for the study of biomolecules, in particular proteins. This knowledge should be also related to the applications in different fields, including food area.

D2 - Ability to apply knowledge: The student should be able to apply the acquired knowledge, in an appropriate and flexible way, also by the development of dedicated high-resolution mass-spectrometry based projects, for the characterization of complex protein mixtures.

D3 - Autonomy of judgment: The students will have to apply the knowledge acquired during the course, to develop an experimental project in the proteomic field, also through the choice of the most appropriate analytical strategies.

D4 - Communication skills: The students must be able to communicate clearly with a correct property of language and terminological rigor their conclusions.

D5 - Learning skills: The students will have to develop learning skills that will enable them to continue studying in a self-directed or autonomous way.

Information for students with disabilities and/or Specific Learning Disabilities (SLD)

To guarantee equal opportunities and in compliance with the laws in force, interested students can ask for a personal interview in order to plan any compensatory and/or dispensatory measures, based on the didactic objectives and specific needs.

Classroom Lectures: 35 hours in classroom

Laboratory Training: 15 hours will be focused on the use of the mass spectrometer and bio-informatics softwares for the characterization of protein and peptide mixtures. 

The students should have basic knowledge of:

- protein chemistry

- liquid chromatography and electrophoresis

- mass spectrometry

Attendance to the course is mandatory (at least 70% of the total number of hours of the course)

Introduction. Review about the amino acids characteristics and properties, peptide bond and proteins. Post-translational modifications. From proteins to the proteome. Proteome Complexity and variability. Proteome characterization: the proteomics era. Proteins Expression and Functional Proteomics. Relationship between proteomics and the other omics sciences. Overview on the analytical techniques used in proteomics.

Mass spectrometry for peptides and proteins. Review of the basic concepts of mass spectrometry. ESI and MALDI ionization. Tandem Mass Spectrometry (MS/MS). Characterization of the peptide sequence by MS/MS. Characterization of the amino acid sequence of a protein by MS-based approaches. Interpretation of the MS/MS data: de novo sequencing.

Proteomics Strategies. Sample preparation: Proteins extraction from the sample. Top-down, middle-down and bottom-up proteomic approaches. Gel-based and gel-free approaches. Protein databases. Protein identification by mass spectrometry: Mascot and PEAKS software. Quantitative Proteomics: SILAC, ICAT and iTRAQ approaches; label-free approaches. Analysis of post-translational modifications. Examples and practical applications.

Outline of Bioinformatics applied to the study of protein sequences. Alignment methods of protein sequences. The Dot Matrix and the Substitution Matrices. Similarity search in databases by heuristic algorithms: FASTA and BLAST. Multiple sequence alignment: the ClustalW software.

1) Proteomica – T. Alberio; M. Fasano; P. Roncada; EDISES

2) Computational Methods for Mass Spectrometry Proteomics – I. Eidhammer; K. Flikka; L. Martens; S.O. Mikalsen; WILEY

3) Proteomics in Practice: A Laboratory Manual of Proteome Analysis – R. Westermeier;  T. Naven; WILEY

The exam is usually an oral test, but in some cases it may also include a preliminary written exam. The oral examination focuses on the discussion of the written test and on other parts of the program that were not covered by the written test. The exam is aimed at verifying the knowledge and skills acquired by the student, his ability to connect the various topics covered during the lessons, and his ability to use appropriate language.

The final evaluation grade is in the 30/30 range.

Evaluation scale:

Unsuitable

Knowledge and understanding of the topic: Important deficiencies

Analysis and synthesis skills: irrelevant, too general

Scientific Language properties: completely inappropriate

18-20

Knowledge and understanding of the topic: basic and with many limitations

Analysis and synthesis skills: just sufficient

Scientific Language properties: just appropriate

21-23

Knowledge and understanding of the topic: slightly more than sufficient knowledge

Analysis and synthesis skills: fair analysis and synthesis skills; student argues logically but basic.

Scientific Language properties: basic

24-26

Knowledge and understanding of the topic: good knowledge

Analysis and synthesis skills: the student has good analysis and synthesis skills; the arguments are presented coherently

Scientific Language properties: The student uses the correct scientific language

27-29

Knowledge and understanding of the topic: more than good knowledge

Analysis and synthesis skills: The student has a notable analysis and synthesis skills

Scientific Language properties: The student has studied the topics in-depth and uses the scientific language properly

30-30 cum laude

Knowledge and understanding of the topic: excellent knowledge

Analysis and synthesis skills: The student has notable analysis and synthesis skills.

Scientific Language properties: The student has studied the topics in-depth, and shows a noticeable problem-solving capacity using the scientific language properly.

link: http://www.dsc.unict.it/corsi/lm-54-org/esami

link: http://www.dsc.unict.it/docenti/vincenzo.cunsolo

Bottom-up and top-down proteomic approaches

LC-ESI MS/MS analysis of peptide mixtures

Interpretation of a MS/MS spectrum of a peptide

Searching protein databases using MS data

Searching for protein sequence similarity