Aim of the course

In this course you will be introduced to the theoretical aspects of the analysis of proteins/peptides by mass spectrometry and gain hands on experience in sample preparation. You will be acquainted with the different workflows of the EMBL proteomics core facility. For a quantitative comparison across samples you will learn how to perform an in-solution digest using Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) (Hughes et al., Molecular Systems Biology, 2014). This workflow enables the efficient removal of detergents and salts from proteins, which are captured by magnetic beads. Following a tryptic cleavage of proteins, you will chemically label the resulting peptides with tandem mass tag (TMT) reagent. You will measure your samples using LC-MS/MS and you will learn in a session focused on the bioinformatics analysis how your acquired data will be analyzed using MS-Fragger and our in house bioinformatics analysis pipeline. In summary, you will gain an overview of our state of the art tool box and you will learn how to take advantage of our services to fuel your scientific projects.

Content

• Flashtalks from participants
• Sample preparation (cell lysis, digestion and TMT labeling)
• Measurement of your prepared samples
• Lectures
  • Mass spec theory
  • Pitfalls in sample preparation
  • Phosphoproteomics
  • Quantitative proteomics
• Data analysis
  • From raw files to spreadsheet tables
  • What data tells you about your workflow
  • Differential abundance analysis
• Social event
  • Finish up with BBQ

Lecturer and teachers

• Mikhail Savitski
• Mandy Rettel
• Per Haberkant
• Jennifer Schwarz
• Frank Stein
• Dominic Helm (DKFZ)

Bookings