Proteomics

A.A. 2023/2024
6
Crediti massimi
56
Ore totali
SSD
BIO/10
Lingua
Inglese
Obiettivi formativi
Scopo dell'insegnamento è che i partecipanti acquisiscano:
·Le conoscenze relative ai concetti di base di proteomica e metabolomica, spettrometria di massa, dei diversi tipi di strumenti e delle numerose tecniche quantitative di proteomica e metabolomica;
·Gli strumenti cognitivi necessari per comprendere i vantaggi e gli svantaggi dei diversi approcci in relazione ad es. al carico di lavoro manuale, costi, sensibilità e scalabilità degli esprimenti
·La capacità di valutazione critica di un work-flow proteomico standard, a partire dalla preparazione del campione, sino a all'acquisizione di dati spettrometria di massa e alla loro analisi ed interpretazione
·Le competenze base per l'analisi e il processamento di dati di spettrometria di massa sperimentali acquisiti, come la loro conversione in formati standard, il controllo di qualità e l'identificazione delle proteine/metaboliti attraverso diversi algoritmi disponibili
·La conoscenza delle applicazioni di proteomica e metabolomica in biomedicina e biologia
Risultati apprendimento attesi
I risultati dell'apprendimento da parte degli studenti vengono valutati dai docenti tramite una prova scritta di esaminazione dell'apprendimento delle metodologie proteomiche e metabolomiche e nel loro utilizzo sulla base del programma svolto durante il corso.
L'esaminazione degli studenti da parte del docente sarà principalmente volta alla valutazione della conoscenza e comprensione delle tecniche proteomiche, metabolomiche e analisi dei dati ed alla valutazione delle competenze acquisite dallo studente al completamento dell'insegnamento stesso. In particolare, sarà valutata la proprietà di linguaggio utilizzata dallo studente, e le competenze acquisite per discriminare la scelta delle diverse metodologie e la loro eventuale integrazione da applicare a diverse problematiche scientifiche.
Corso singolo

Questo insegnamento può essere seguito come corso singolo.

Programma e organizzazione didattica

Edizione unica


Programma
· Introduction to proteomics: definition and concepts, history, challenges
· Protein fractionation, separation, purification and quantification
· Protein extraction and sample preparation prior to MS
· Introduction to liquid chromatography (LC) separation
· Mass spectrometry (MS) fundamentals I
o Soft Ionization techniques (MALDI/ESI)
o Concepts of mass accuracy and resolution
o An overview on modern Mass Analyser design
· Mass spectrometry (MS) fundamentals II
o Tandem mass spectrometry
o Peptide fragmentation
o Protein de novo sequencing
· Protein Identification by probability-based scoring through search engines
· Shot-gun proteomics workflows and considerations
· Quantitative proteomics:
o Label-free and isotopic-label-based strategies
o Targeted proteomics (webinar)
· Protein post-translational modifications
o Tailored Strategies (biochemical and analytical)
o Examples (phospho-proteomics, methyl-proteomics)
· Interaction proteomics: principles and examples (protein-protein, protein-nucleic acid interactions)
· Structural proteomics and conformational proteomics (External Seminar)
· Automated analysis of MS data for peptide and protein ID (External Seminar)
· Proteomics application in cell biology (case-studies)
· Translational proteomics:
o Proteome profiling of clinical samples
o Proteomics of body fluids (serum, urine, etc)
o Proteomics in drug development (e.g chemo-proteomics, thermal protein profiling, etc)
· Proteomics and systems biology:
· - Feature selection​
· - Overrepresentation and GeneSet Enrichment Analysis​
· - Basics of graph theory and application to protein networks​
· - Classifiers and predictors for clinical applications (biomarkers, prognostic and drug response predictors, surrogate outcomes) (focus seminar) ​

· Metabolomics: definitions and approaches
· Sample preparation for metabolomics.
· Targeted and untargeted metabolomics approach. Typical metabolomic analysis workflows. Identification of metabolites. Metabolite databases.
· Univariate and Multivariate analyses of data: introduction to chemometry.
· Metabolomics and Systems Biology
· The dynamic study of metabolism: Fluxomics
· Applications of metabolomics in pre-clinical research
· Applications of Metabolomics in the clinics
Prerequisiti
Basic knowledge of chemistry and biochemistry. Notions on the nature and structure of proteins.
Basic knowledge of principle protein separation techniques (e.g. chromatography, electrophoresis, etc)
Metodi didattici
Lectures will be accompanied by hands-on laboratory work, during which the experiments carried out in the laboratory session will reinforce the concepts presented in the lectures. Practicals will also include computer work, through small computational tutorials carried out in small groups, with the following assignments: mass spectrum interpretation for peptide sequence reconstruction; launch of a protein ID search engine and discussion on data output; statistical and functional analysis of a quantitative proteomics experiment with MaxQuant/Perseus.
Class discussion will be also organized with presentation of real cases of proteomics and metabolomics studies, during which
students are required to actively interact.
Live discussions and questions during lectures and tutorials are highly encouraged.
Materiale di riferimento
Students will be provided with the slides of the course, which must be suitably integrated with lecture notes.
With regard to the proteomics and metabolomics parts, mainly due to the rapid evolution that characterizes these disciplines, there are few texts on the market that include all the topics covered, adequately up-to-date.
Possible reference textbooks for proteomics and metabolomics are:

Proteomica T. Alberio, M. Fasano, P. Roncada, 2021 EdiSES (in Italian)
Proteomics for Biological Discovery, Second Edition Timothy D. Veenstra, John R. Yates III Print ISBN:9781118279243 |Online ISBN:9781119081661 |DOI:10.1002/9781119081661 © 2019 John Wiley & Sons, Inc.
Introducing Proteomics, from concepts to sample preparation, mass spectrometry and data analysis by J. Lovric (2011), Wiley-Blackwell Publishers 
Introduction to proteomics, Principles and Applications (2010) N. Mishra, John Wiley & Sons, Inc., Publication.
Metabolomics: From Fundamentals to Clinical Applications (2017) A. Sussulini, Springer.
Metabolomics in Practice: Successful Strategies to Generate and Analyze Metabolic Data (2013). M. Lämmerhofer and W. Weckwerth, Wiley‐VCH Verlag GmbH & Co. KGaA.
These textbooks will be then integrated with relevant recent reviews/articles on the topics covered during the lectures.
Video lectures and tutorials from past International Schools/Courses of proteomics and freely available online will also be indicated to the students
Modalità di verifica dell’apprendimento e criteri di valutazione
Given the highly interactive nature of the course, which includes practical and bioinformatics exercises, case studies and group work, it is essential to attend lessons regularly. Students who have followed at least 80% of the course are considered attending.
The overall assessment of the students will be based on their performance in a compulsory oral test, consisting of questions aiming at verifying the overall understanding of the basic principles of the analytical methods ion applied in MS-based proteomics and metabolomics, the major challenges of these disciplines and the solutions developed to tackled them. Special attention will will be given to assess the understating of the different approaches and strategies in proteomics and metabolomics that are linked to the simulation of real-life scientific situations that embody what has been discussed in the course. The exam will also verify the students' understating of the most important data analysis approachess, including statistical analysis of large-scale, quantitative -omics data.
BIO/10 - BIOCHIMICA - CFU: 6
Esercitazioni: 16 ore
Lezioni: 40 ore
Docente/i
Ricevimento:
per appuntamento, da fissare via email o telefono
Edificio 13, piano 1 del Dipartimento di Oncologia Sperimentale, Istituto Europeo di Oncologia, Via Adamello 16, 20139 Milano
Ricevimento:
Su appuntamento telefonico o e-mail
Via Balzaretti 9, 20113 Milano