Protein mass spectrometry and proteomics
Summary
In systems biology, proteomics represents an essential pillar. The understanding of protein function and regulation provides key information to decipher the complexity of living systems. Proteomic technology now enables deep quantitative proteome mapping via mass spectrometry.
Content
1. Introduction and mass spectrometry
Introduction to protein analysis and proteomics; Reminders in mass spectrometry; Why proteomics and mass spectrometry?; Ionization sources, analyzers, and detectors used in proteomics
2. Mass spectrometry-based proteomic strategy and workflows
Bottom-up versus top-down strategies; Sample preparation
3. Separations techniques in proteomics
Gel electrophoresis; Isoelectric focusing; Liquid chromatography (RP, IEX)
4. Quantitative proteomic workflows using mass spectrometry
Label-free methods; Labelling-based techniques; Other quantitative techniques
5. Proteomic bioinformatics
Databases; Identification of protein; Quantification of proteins; Bioinformatics tools; Practical examples
6. Applications to biology and clinical research
What strategy?; Experimental design; Biomarker discovery; Population proteomics; Forensics; Targeted mass spectrometry-based approaches; Other biological applications of mass spectrometry; Lab visit at Nestlé Research by group of 5-10 students
Keywords
Mass Spectrometry; Liquid Chromatography; Electrophoresis; Proteins; Peptides; Systems Biology; Bioinformatics; Human Samples; Clinics; Isotopic Labelling; Quantification
Learning Prerequisites
Recommended courses
CH-210 Biochimie I
CH-301 Méthodes de séparation analytiques
CH-314 Structural analysis
Important concepts to start the course
Mass spectrometry; Biochemistry
Learning Outcomes
By the end of the course, the student must be able to:
- Differentiate biological mass spectrometry techniques to identify and quantify proteomes
- Distinguish the main separation techniques for proteins and peptides
- Choose appropriate methodology for protein analysis
- Discuss literature related to proteomics
- Describe the field of applications of proteomics and expand those concepts beyond, e.g., to metabolomics
- Interpret some mass spectrometry data
Teaching methods
Ex-cathedra
Assessment methods
Written exam with Multiple Choice Questions (MCQ) (2/3) & exercices (1/3)
Supervision
| Office hours | No |
| Assistants | No |
| Forum | No |
Resources
Ressources en bibliothèque
- Quantitative methods in proteomics / Marcus
- LC-MS/MS in proteomics / Cutillas
- Serum/plasma proteomics / Simpson
Références suggérées par la bibliothèque
Websites
- https://www.nature.com/nature/journal/v537/n7620/full/nature19949.html
- https://rd.springer.com/book/10.1007/978-1-61779-885-6/page/1
- https://rd.springer.com/book/10.1007/978-1-60761-780-8/page/1
- http://www.springer.com/gp/book/9781493970568
Moodle Link
Videos
In the programs
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Protein mass spectrometry and proteomics
- Courses: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Protein mass spectrometry and proteomics
- Courses: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Protein mass spectrometry and proteomics
- Courses: 2 Hour(s) per week x 14 weeks
- Type: optional