Proteomics
A.Y. 2021/2022
Learning objectives
"On completion of the course, the student is expected to:
· Acquire the basic concepts of proteomics and metabolomics, and of the most relevant technologies, such as mass spectrometry of the different types of instruments and of the numerous quantitative proteomics and metabolomics techniques;
· Acquire the tools necessary to understand the advantages and disadvantages of the different approaches with regard to manual work load, costs, sensitivity and scalability
· Critically evaluate a proteomics workflow, from sample preparation, to the acquisition of spectra, to data analysis and interpretation
· Carry out raw data analysis on collected measurement raw data, such as conversion to standardized formats, quality control and identification of proteins through search engines
· Account for applications for proteomics and metabolomics in biomedicine and biology
"
· Acquire the basic concepts of proteomics and metabolomics, and of the most relevant technologies, such as mass spectrometry of the different types of instruments and of the numerous quantitative proteomics and metabolomics techniques;
· Acquire the tools necessary to understand the advantages and disadvantages of the different approaches with regard to manual work load, costs, sensitivity and scalability
· Critically evaluate a proteomics workflow, from sample preparation, to the acquisition of spectra, to data analysis and interpretation
· Carry out raw data analysis on collected measurement raw data, such as conversion to standardized formats, quality control and identification of proteins through search engines
· Account for applications for proteomics and metabolomics in biomedicine and biology
"
Expected learning outcomes
"Student learning outcomes will be assessed by the faculty through a written test examining the student's learning of proteomic and metabolomic methodologies and in their use based on the syllabus carried out during the course.
The examination of the students by the lecturer will be mainly aimed at assessing the knowledge and understanding of proteomic and metabolomic techniques and data analysis and at evaluating the skills acquired by the student at the completion of the teaching itself. In particular, it will be evaluated the property of language used by the student, and the skills acquired to discriminate the choice of different methodologies and their possible integration to be applied to different scientific problems.
"
The examination of the students by the lecturer will be mainly aimed at assessing the knowledge and understanding of proteomic and metabolomic techniques and data analysis and at evaluating the skills acquired by the student at the completion of the teaching itself. In particular, it will be evaluated the property of language used by the student, and the skills acquired to discriminate the choice of different methodologies and their possible integration to be applied to different scientific problems.
"
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
More specific information on the delivery modes of training activities for academic year 2021/22 will be provided over the coming months, based on the evolution of the public health situation.
Course syllabus
Course Syllabus:
· 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
- Soft Ionization techniques (MALDI/ESI)
- Concepts of mass accuracy and resolution
- An overview on modern Mass Analyser design
· Mass spectrometry (MS) fundamentals II
- Tandem mass spectrometry
- Peptide fragmentation
- Protein de novo sequencing
· Protein Identification by probability-based scoring through search engines
· Shogun proteomics workflows and considerations
· Quantitative proteomics:
- Label-free and isotopic-label-based strategies
- Targeted proteomics
· Protein post-translational modifications
- Tailored Strategies (biochemical and analytical)
- Examples (phospho-proteomics, methyl-proteomics)
· Interaction proteomics: principles and examples (protein-protein, protein-nucleic acid interactions)
· Structural proteomics: XL-MS strategies and linked challenges
· Protein databases, bioinformatics and data analysis
· Proteomics application in cell biology (case-studies)
· Translational proteomics:
- Proteome profiling of clinical samples
- Proteomics of body fluids (serum, urine, etc)
- Proteomics in drug development (e.g chemo-proteomics, thermal protein profiling, etc)
- Case studies
· Proteomics and systems biology
· 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
· 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
- Soft Ionization techniques (MALDI/ESI)
- Concepts of mass accuracy and resolution
- An overview on modern Mass Analyser design
· Mass spectrometry (MS) fundamentals II
- Tandem mass spectrometry
- Peptide fragmentation
- Protein de novo sequencing
· Protein Identification by probability-based scoring through search engines
· Shogun proteomics workflows and considerations
· Quantitative proteomics:
- Label-free and isotopic-label-based strategies
- Targeted proteomics
· Protein post-translational modifications
- Tailored Strategies (biochemical and analytical)
- Examples (phospho-proteomics, methyl-proteomics)
· Interaction proteomics: principles and examples (protein-protein, protein-nucleic acid interactions)
· Structural proteomics: XL-MS strategies and linked challenges
· Protein databases, bioinformatics and data analysis
· Proteomics application in cell biology (case-studies)
· Translational proteomics:
- Proteome profiling of clinical samples
- Proteomics of body fluids (serum, urine, etc)
- Proteomics in drug development (e.g chemo-proteomics, thermal protein profiling, etc)
- Case studies
· Proteomics and systems biology
· 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
Prerequisites for admission
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)
Basic knowledge of principle protein separation techniques (e.g. chromatography, electrophoresis, etc)
Teaching methods
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 lecture and tutorials are encouraged
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 lecture and tutorials are encouraged
Teaching Resources
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:
· 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
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:
· 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
Assessment methods and Criteria
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 student will be based on their performance in the following aspects:
1) A compulsory written test, consisting of both open questions and multiple choice questions; the open questions will aim to verify the understanding of the principles of different approaches and strategies in proteomics and metabolomics, related to the simulation of real life scientific situations that embody what has been discussed in the course (40%)
2) An oral exam, based on the critical discussion of practical laboratory activities (assignments) and of a scientific article related to the topics addressed during the course (among a portfolio proposed by the teacher), which the students are expected to present and assess critically. During the oral exam the ability to use the specific disciplinary language appropriately and rigorously will be assessed (30%)
3) The class participation, creativity, ability to work in a team, during the practical assignments and activities (30%)
The overall assessment of the student will be based on their performance in the following aspects:
1) A compulsory written test, consisting of both open questions and multiple choice questions; the open questions will aim to verify the understanding of the principles of different approaches and strategies in proteomics and metabolomics, related to the simulation of real life scientific situations that embody what has been discussed in the course (40%)
2) An oral exam, based on the critical discussion of practical laboratory activities (assignments) and of a scientific article related to the topics addressed during the course (among a portfolio proposed by the teacher), which the students are expected to present and assess critically. During the oral exam the ability to use the specific disciplinary language appropriately and rigorously will be assessed (30%)
3) The class participation, creativity, ability to work in a team, during the practical assignments and activities (30%)
BIO/10 - BIOCHEMISTRY - University credits: 6
Practicals: 16 hours
Lessons: 40 hours
Lessons: 40 hours
Professor(s)
Reception:
to be defined by appointment, via email or telephone
Building 13, Floor 1 of the Department of Experimental Oncology of the European Institute of Oncology, Via Adamello 16, Milan
Reception:
By appointment via email