Mass spectrometry-based proteomics
Mass spectrometry-based proteomics
10 February 2026, 9h00-17h00
11 February 2026, 9h00-17h00
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
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.
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.
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.
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.
Simon Devos
Dr. Simon Devos is Head of the Proteomics Core at VIB. He's a proteomics specialist with a keen focus on technology development and implementation, both in the MS-driven and non-MS-driven proteomics field.
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.
Program
Welcome coffee (provided - 5th floor)
Lecture 1: Basics proteomics and sample preparation in room L5
Lecture 2: Mass spectrometry DDA in room L5
Coffee break and flash talks on 5th floor
Lab session 1: Hands on sample preparation on S-trap from protein extraction to digest in lab on 2nd floor
Lecture 3: DDA data analysis theory in room L5
Lunch (provided - 5th floor)
Lab session 2: Peptide elution in lab on 2nd floor
Demo session 1: DDA tutorial in room L4
Coffee break (provided - 5th floor)
Lab session 3: Peptide clean-up and guided tour in mass spec suite in lab on 2nd floor
Closing Remarks in lab on 2nd floor
Welcome coffee break (provided - 5th floor)
Dissolve peptides/Trinean explanation in lab on 2nd floor
Lecture 4: theory DIA in room L5
Coffee break (provided - 5th floor)
Lecture/ Demo session 2: Data analysis DIA in room L4
Lunch (provided - 5th floor)
Demo session 2: Statistical analysis in room L4
Coffee break (provided - 5th floor)
Demo session 2: Statistical analysis in room L4
Closing remarks
Practical info
10 February 2026 - 11 February 2026
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
10 February 2026 - 11 February 2026
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
10 February 2026 - 11 February 2026
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
10 February 2026 - 11 February 2026
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.