Mass spectrometry based proteomics

Mass spectrometry is an advanced analytical technique for accurate mass measurement. It does so by producing charged molecular species in vacuum followed by its separation in the magnetic and electric fields on the basis of their mass to charge (m/z) ratio. MALDI and ESI- coupled with mass analyzers are commonly used mass spectrometer configuration in proteomics. The human proteome draft was decoded by using high-resolution liquid chromatography coupled with mass spectrometry.

In this module, we will discuss the basics of mass spectrometry, sample preparations, liquid chromatography, hybrid mass spectrometers and quantitative proteomics techniques such as iTRAQ, SILAC and TMT using mass spectrometry. The course will also provide the basic knowledge about sample preparation, mass spectrometry workflow, different chromatography technologies and quantitative proteomics.

Week 1: Proteomics introduction and sample preparation

Lec 1: Introduction to proteomics
Lec 2: Why proteomics and sample preparation
Lec 3: Protein extraction
Lec 4: In-gel & in-solution digestion
Lec 5: Fundamentals of mass spectrometry

Week 2: Basics of mass spectrometry

Lec 6: Chromatography technologies
Lec 7: Liquid chromatography
Lec 8: Mass spectrometry: Ionization sources
Lec 9: Mass spectrometry: Mass analyzers
Lec 10: MALDI sample preparation and analysis

Week 3: Quantitative proteomics

Lec 11: Introduction to quantitative proteomics
Lec 12: Hybrid mass spectrometry configurations
Lec 13: SILAC: In vivo labeling
Lec 14: iTRAQ: In vitro labeling
Lec 15: TMT: In vitro labeling

Week 4: Proteomics and systems biology

Lec 16: Quantitative proteomics data analysis
Lec 17: Proteomics and systems biology-I
Lec 18: Proteomics and systems biology-II
Lec 19: Proteomics applications
Lec 20: Challenges in proteomics