Advanced Proteomics and Metabolomics
Objectives
Course Objectives:
1. To provide students with a fundamental understanding of mass spectrometry-based data acquisition techniques for proteomics and metabolomics.
2. To introduce students to advanced mass spectrometry-based data analysis techniques for proteomics and metabolomics.
3. To equip students with the ability to interpret and analyze proteomics and metabolomics data sets using computational tools.
4. To teach students how to apply statistical methods to proteomics and metabolomics data analysis to identify significant changes in protein and metabolite expression.
5. To train students on how to perform data processing and analysis for various types of mass spectrometry-based experiments, such as label-free and isobaric labeling approaches.
6. To provide students with an understanding of the biological significance of the data generated from mass spectrometry-based experiments and how to interpret the results.
7. To enable students to understand how mass spectrometry can pin point post translations modification.
8. To prepare students to design and implement mass spectrometry-based experiments and analyze the resulting data in order to answer biological questions in proteomics and metabolomics.
9. To enable students to critically evaluate published proteomics and metabolomics data and assess their relevance to specific research questions.
Overall, the course strives to provide students an improved comprehension of the biological context in which the data are produced, as well as the technical knowledge and practical skills required for effective mass spectrometry-based data analysis in proteomics and metabolomics.
General characterization
Code
12499
Credits
3.0
Responsible teacher
Rune Matthiesen
Hours
Weekly - Available soon
Total - Available soon
Teaching language
Português
Prerequisites
Recommended requirements, not necessarily mandatory:
A Bachelor''s degree in a relevant field such as biochemistry, molecular biology, biotechnology, chemistry, or a related discipline.
1. Prior coursework in bioinformatics, mass spectrometry principles, protein biochemistry and protein separation techniques.
2. Basic knowledge of statistics, including hypothesis testing, regression analysis, and experimental design.
3. Familiarity with programming languages such as R or Python, including data visualization and statistical analysis tools.
4. A laptop for hands-on exercises.
Bibliography
Available soon
Teaching method
Available soon
Evaluation method
Available soon
Subject matter
Program detail:
From 9.30 AM to 2 PM on Tuesdays starting 29th of April.
29th of April
(FCT, Lab 120 Ed II) - To be confirmed
Database dependent searches
9.30-12.00 T: Overview of MS-based proteomics applications
12.30-14.00 P: Peak processing, de novo sequencing
6th of May
(In ITQB room 3.19 - To be confirmed) UniMS metabolomics. Lecture and practical session more focused on instrumentation.
Fundamentals of metabolomics (Profs. Luís Gonçalves, Ana Guerreiro)
13th of May
(In ITQB room 3.19) UniMS proteomics. Lecture and practical session more focused on instrumentation.
Fundamentals of proteomics (Profs. Isabel Abreu, Ricardo Gomes, Bruno Alexandre)
20th of May
(FCT, Lab 120 Ed II)
MSMS search engines
9.30-12.00 T: Database dependent searches
12.30-14.00 P: MaxQuant and SearchGui, FDR
27th of May
(FCT, Lab 120 Ed II)
Quantitative proteomics
9.30-12.00 T: Overview of quantitative methods
12.30-14.00 P: Label free and stable isotope labeling based quantitation
3rd of June
(FCT, Lab 120 Ed II)
Post translational modifications (PTMs)
9.30-12.00 T: Overview of post translation modification analysis
12.30-14.00 P: Phospho proteomics analysis
11th of June (exam)
Written test
References:
Proteomics:
https://drive.google.com/file/d/16VoJZHMRIE9YIMJzGfVgtsNojLNR1kgu/view?usp=share_link
Metabolomics:
https://drive.google.com/file/d/1A-O8a766kVrrtHqUaZ0rnT-OwRXoxV6L/view?usp=share_link
Programs
Programs where the course is taught: