Basic proteomics
Basic proteomics
5 February 2025, 9h00-17h00
6 February 2025, 9h00-17h00
General context
The VIB Proteomics Core offers contemporary mass spectrometry (MS)-based proteomics services to VIB scientists. During this course we provide lectures on the basic principles and theory behind MS-based proteomics.
The goal is to provide participants with insight on how to design their experiments and how to select the right sample preparation procedure and labeling strategy.
During the hands-on lab sessions, participants will be trained in sample preparation including protein extraction, digestion and peptide clean-up for LC-MS/MS analysis.
We also include a data analysis demonstration session, covering critical steps in proteomics data analysis including protein identification, quantification, statistical analysis and data visualization.
This training will be a combination of theoretical lectures, hands-on lab sessions and data analysis demonstrations. There will also be a guided tour in the VIB Proteomics Core facility.
This course is aimed at users of the VIB Proteomics Core and/or any VIB scientists that are planning to work with the core facility in the near future. Check out their services.
Freeware MaxQuant, DIA-NN and Perseus.
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
Introduction of theoretical concepts
- Basic proteomics and mass spectrometry principles
- Key steps in proteomics sample preparation
- How to choose the right protocol for your project
- Experimental design and basic data analysis principles
Hands-on sample processing and data analysis demonstration
- Hands-on sample preparation by suspension trapping, including protein extraction, reduction/alkylation, digestion and peptide clean-up
- Analyzing peptide samples by LC-MS/MS
- Launching a database search in MaxQuant
- Launching a DIA data analysis in DIA-NN
- Data interpretation and basic statistics in Perseus
8h30-9h00 Coffee on 5th floor
9h00-10h15 Lecture 1: Basics proteomics and sample preparation in room L5
10h20-11h00 Lecture 2: Mass spectrometry DDA in room L5
11h00-11h15 Coffee break and flash talks on 5th floor
11h15-12h15 Lab session 1: Hands on sample preparation on S-trap from protein extraction to digest in lab on 2nd floor
12h15-13h Lecture 3: DDA data analysis theory in room L5
13h00-13h45 Lunch on 5th floor
13h45-14h15 Lab session 2: Peptide elution in lab on 2nd floor
14h15-15h15 Demo session 1: DDA tutorial in room L4
15h15-15h30 Coffee break on 5th floor
15h30-16h45 Lab session 3: Peptide clean-up and guided tour in mass spec suite in lab on 2nd floor
16h45-17h00 Closing Remarks in lab on 2nd floor
8h30-9h00 Coffee on 5th floor
9h00-9h30 Dissolve peptides/Trinean explanation in lab on 2nd floor
9h30-10h45 Lecture 4: theory DIA in room L5
10h45-11h00 Coffee break on 5th floor
11h00-13h00 Lecture/ Demo session 2: Data analysis DIA in room L4
13h00-13h45 Lunch on 5th floor
13h45-15h00 Demo session 2: Statistical analysis in room L4
15h00-15h15 Coffee break on 5th floor
15h15-16h30 Demo session 2: Statistical analysis in room L4
16h30-16h45 Closing remarks
Practical info
05 February 2025 - 06 February 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
05 February 2025 - 06 February 2025
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
05 February 2025 - 06 February 2025
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.
05 February 2025 - 06 February 2025
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.
05 February 2025 - 06 February 2025
Ghent - VIB/UGent FSVM II
room L5 and L4 of the FSVM2 building, Technologiepark, Gent