Mass spectrometry-based proteomics
Mass spectrometry-based proteomics
to be announced
General context
This introductory course helps you get familiar with the principles and workflows of mass spectrometry-based proteomics. Designed for researchers new to the field, the training covers the complete pipeline - from experimental design and sample preparation to data analysis and basic data interpretation.
You will gain practical experience with essential techniques such as protein extraction, digestion, and peptide cleanup, and learn to analyze proteomics datasets using standard bioinformatics tools.
- Describe key concepts and fundamental principles of mass spectrometry-based proteomics
- Explain the rationale behind sample preparation methods and protocol choices
- Perform protein extraction, digestion, and peptide clean-up using standard workflows
- Analyze example datasets for protein identification and quality assessment using basic bioinformatics tools
- Assess the suitability of proteomics approaches for different research questions
The training combines theoretical sessions with hands-on lab work and guided demonstrations of data analysis. Participants will begin with an introduction to basic proteomics concepts and principles, followed by practical sessions. In addition, participants will tour the VIB Proteomics Core facility and learn best practices in experimental design and workflow planning.
Basic familiarity with R is recommended for the data interpretation session. Participants without prior experience should contact janick.mathys@vib.be to secure a spot in our R introduction training before attending.
- MaxQuant (protein identification and quantification)
- DIA-NN (data-independent acquisition analysis)
- R packages: msqrob2, limma
This course is part of the learning path Bulk proteomics data.
AI methods used
AI and machine learning are used in a limited, applied way within the data-analysis part of the course: participants are exposed to DIA-NN, which uses neural-network/ deep-learning models to support peptide and protein identification and quantification in DIA proteomics data.
Participants will begin with an introduction to basic proteomics concepts and principles, followed by practical sessions focusing on:
- sample preparation: suspension trapping workflow including protein extraction, reduction/alkyalation, digestion, and peptide clean-up
- data acquisition: peptide analysis by LC-MS/MS
data analysis: launching database searches in MaxQuant, performing DIA data analysis in DIA-NN, basic interpretation and visualization of results using R
Trainers
Katie Boucher
Katie Boucher is a proteomics technician at the VIB Proteomics Core and lab manager at the Impens lab. She focuses on molecular cloning, organization of research tools, and she is running one of the mass spectrometers in the Core.
Sara Dufour
Sara Dufour is proteomics bioinformatician at the VIB Proteomics Core. Next to running one of the mass spectrometers in the Core, she is responsible for data analysis of most projects along with testing and maintaining of different data analysis workflows.
Teresa Maia
Dr. Teresa Maia is a bioinformatics data scientist at the VIB Proteomics Core. She works on the implementation of data analysis workflows, with a special focus on automatization of data processing and creation of data sharing solutions.
An Staes
An Staes is mass spectrometry proteomics expert at the Proteomics Core at VIB and VIB Center for Medical Biotechnology. Her research focuses on implementing and developing mass spectrometry driven methodologies in proteomics.
Evy Timmerman
Evy Timmerman is a mass spectrometry and proteomics expert at the VIB Proteomics Core. Next to running one of the mass spectrometers in the Core, she is involved in data analysis of standard projects as well as N-terminomics approaches for which she is combining different data analysis workflows and software tools.
Delphi Van Haver
Delphi Van Haver is a proteomics expert at the VIB Proteomics Core. She is the main responsible for proteomics sample preparation and implementation of new sample preparation protocols at the Core.