Course Package in Mass Spectrometry-Based Proteomics

29 October + 5 November 2021

Dr. Manfredo Quadroni, UNIL; Dr. Patrice Waridel, UNIL

Dr. Manfredo Quadroni, UNIL; Dr. Patrice Waridel, UNIL

The goal of the first part is to give some basic theoretical and practical knowledge on the mass spectrometry (MS) techniques used in proteomics to identify proteins in simple and complex mixtures. It will cover the following subjects: • Fundamental concepts of mass spectrometry (MS) of peptides and proteins • Strategies for protein identification with MS data: theory, concepts, variants • Database searches with MS data: practical examples and exercises • Validation and interpretation of results. The goal of this second part is to give more advanced theoretical and practical knowledge on the mass spectrometry (MS) techniques used in proteomics, in particular for the characterization of post-translational modifications (PTMs) and the quantitation of protein in complex mixtures. It will cover the following subjects: • Strategies for PTM identification in proteins by MS: theory and concepts • PTM data analysis practical examples and exercises: phosphorylation • Quantitation of proteins by MS: labeled and unlabeled strategies • Quantitative workflows and examples of applications.

1st day Introduction course - Schedule

09:00 Start – organizational issues09:10 Introduction, MS of proteins and peptides
10:00 De novo exercise
10:30 coffee break
11:00 De novo exercise correction
11:15 Protein ID by MS - part I
12:15 MASCOT exercise

12:45 -------LUNCH-------------

13:45 MASCOT exercise correction
14:00 Protein ID by MS - part II
15:00 Break
15:15 Protein complex analysis (Scaffold) exercise
16:30 Correction of exercise, Q&A
17:00 End

2nd day Advanced course - Schedule

09:00 Start – Reminder
09:10 Post Translational Modification (PTM) analysis
10:00 coffee break 10:30 Proteomics : challenges and deliverables
11:00 Quantitative proteomics

12:45 -------LUNCH-------------

13:45 Quantitative proteomics –exercise part I
14:45 Quantitative proteomics –exercise part II
15:30 Break 16:00 Quantitative proteomics exercise : correction/discussion
16:30 Conclusions
16:45 End

Université de Lausanne, Amphipôle 336

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