Basic Proteomics
26 and 27 October
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
Francis Impens
Dr. Francis Impens is Professor of Protein Chemistry at Ghent University and Group Leader and Head of the Proteomics Core at VIB. His research focuses on functional proteome analysis by mass spectrometry and its application to study host-bacteria interactions.
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.
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.
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.
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
10h20-11h15 Coffee break and flash talks on 5th floor
11h20-12h45 Lab session 1: Hands on sample preparation on S-trap from protein extraction to digest in lab on 2nd floor
12h45-13h45 Lunch on 5th floor
13h45-14h15 Lab session 2: Peptide elution in lab on 2nd floor
14h15-15h15 Lecture 2: Mass spectrometry and data analysis in room L5
15h15-15h30 Coffee on 5th floor
15h30-16h00 Lab session 3: Peptide clean-up and guided tour in mass spec suite in lab on 2nd floor
16h00-16h30 Questions or discussion – Closing Remarks in lab on 2nd floor
8h30-9h00 Coffee on 5th floor
9h00-10h00 Dissolve peptides/Trinean explanation- guided tour in mass spec suite in lab on 2nd floor
10h05-11h45 Lecture/ Demo session 1: Data analysis DDA in room L4
11h45-12h00 Coffee on the 5th floor
12h00-13h00 Lecture/ Demo session 2: Data analysis DIA in room L4
13h00-14h00 Lunch on the 5th floor
14h00-16h00 Demo session 2: Statistical analysis in room L4
16h00-16h15 Closing remarks
Practical info
26 October 2023 - 27 October 2023
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
26 October 2023 - 27 October 2023
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.
26 October 2023 - 27 October 2023
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket and have it validated at the reception desk of the FSVM building. Parking will only be allowed in regular parking spots (for instance in front of the building) and in the new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited and after initial warnings, fines will be issued (€ 50).
26 October 2023 - 27 October 2023
Ghent - VIB/UGent FSVM II
room L5 of the FSVM2 building, Technologiepark, Gent