BePa@VIB Proteomics Summer School
BePa@VIB Proteomics Summer School
Mo 26/08/2024 - Fr 30/08/2024
General context
Many researchers use proteomics as a research tool. BePA (Belgian Proteomics Association) is organizing workshops for these users in collaboration with VIB. A broad selection of proteomics experts will go through the entire workflow from sample preparation, over data acquisition to data analysis. At the end of the course, attendees will better understand the dos and don’ts in proteomics and be able to design their own experiment in order to find an answer to their protein-related questions.
This summer school is organized with the support of VIB, the Doctoral School of Ghent University and Thermo Fisher Scientific.
! Cancellations must be done before July 1st. Later cancellations will be subject to a cancellation fee of €50 !
The summer school will show researchers what the capabilities of proteomics are. By focusing on the different steps of a robust experimental design, they will learn the shortest route to answer their biological questions on proteins.
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.
Daria Fijalkowska
Dr. Daria Fijalkowska is an omics data analyst at VIB Center for Medical Biotechnology in Gent. She obtained her PhD at Ghent University, where she combined proteomics with ribosome profiling and RNA sequencing to study alternative translation initiation. During her postdoc at DKFZ Heidelberg she characterized epigenetic protein complexes in mixed lineage leukemia. Afterwards, she returned to Belgium as a staff scientists tackling bioinformatics data analysis.
Enrico Massignani
Enrico earned his PhD in 2021 with a thesis on computational methods to research protein arginine methylation and other PTMs by mass spectrometry, under the supervision of Dr Tiziana Bonaldi at the European School of Molecular Medicine (Milan, Italy). He is currently working as a Postdoc at the Flanders Institute for Biotechnology, in the CompOmics group led by Prof Lennart Martens. His research mainly focuses on understanding the effects of PTMs on a protein’s structure and function and how different PTMs can interact with each other.
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.
Gerben Menschaert
Dr. Gerben Menschaert is Guest Professor at the Faculty of Bioscience Engineering within the BioBix Lab for Bioinformatics and Computational Genomics. His research focusses on integration of mass spectrometry and sequencing in a proteogenomics setup.
Kris Gevaert
Dr. Kris Gevaert is Senior Full Professor of Proteomics at Ghent University, and Science Director a.i. and Group Leader at the VIB Center for Medical Biotechnology.
Lieven Clement
Lieven Clement is an Associate Professor of Statistical Genomics at Ghent University. His research focuses on developing statistical methods and open-source tools for differential omics data analysis.
Maarten Dhaenens
Dr. Maarten Dhaenens is Executive PI at ProGenTomics (Lab of Pharmaceutical Biotechnology) and President of the Belgian Proteomics Association
Marcel Bühler
Dr. Marcel Bühler is a postdoctoral researcher in the group of Prof. Kris Gevaert at VIB-CMB. After obtaining his PhD in Cancer Biology from the University of Zurich, where he used mass spectrometry-based proteomics to study human brain tumors, he joined VIB to establish workflows for ultra-low input and single-cell proteomics.
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.
Sven Eyckerman
Dr. Sven Eyckerman is Associate Professor at Ghent University and Expert Scientist at the VIB. His team focuses on tools and technologies for the study of human protein complexes.
Tine Claeys
Tine Claeys is a last-year PhD, soon postdoc, in the CompOmics group of Prof. Martens. During her PhD she mainly focused on the reuse of public proteomics data to uncover tissue-specific protein and PTM patterns from a machine learning perspective. In parallel, she is engaging the proteomics community to improve metadata annotation and the AI-oriented reusability of public proteomics data.
Program
- Day 1: Basic concepts-Sample preparation-Experimental design-Data dependent acquisition concepts
- Day 2: Data dependent acquisition: identification
- Day 3: Data independent acquisition: basic concepts & data analysis
- Day4: Quantification
- Day 5: Proteomics applications
8h15-9h00 Registration and good morning coffee
9h00-9h15 Welcome (An Staes)
9h15-9h45 Basic concepts of LC-MS driven proteomics (Francis Impens)
9h45-10h45 Sample preparation: the basics (Francis Impens)
10h45-11h15 BREAK
11h15-12h15 Experimental design (Lieven Clement)
12h15-13h00 Flash presentation (1min/person)
13h00-14h00 LUNCH
14h00-15h00 LC separation in LC-MS (Jeff Op De Beeck Sponsored talk Thermo Fisher Scientific)
15h00-15h30 BREAK
15h30-16h45 Data dependent acquisition: the basics and instrument design (An Staes)
8h15-9h00 Registration and good morning coffee
9h00-10h00 DDA: The theory of identification (Tine Claeys)
10h00-10h30 BREAK
10h30-12h00 DDA ID: practical (Tine Claeys, Pathmanaban Ramasamy, Enrico Massignani)
12h00-13h00 LUNCH
13h00-14h30 DDA ID: practical II (Tine Claeys, Pathmanaban Ramasamy, Enrico Massignani)
14h30-15h00 BREAK
15h00-17h00 DDA ID: practical III (Daria Fijalkowska)
8h15-9h00 Registration and good morning coffee
9h00-10h30 Data Independent acquisition: the basics (Maarten Dhaenens & An Staes)
10h30-11h00 BREAK
11h00-12h30 DIA: Data analysis (Maarten Dhaenens & An Staes)
12h30-13h30 LUNCH
13h30-15h00 DIA ID: practical I (Maarten Dhaenens & An Staes)
15h00-15h30 BREAK
15h30-17h00 DIA ID: practical II (Maarten Dhaenens & An Staes)
8h15-9h00 Registration and good morning coffee
9h00-10h00 DDA: Quantification I - Background on preprocessing (Lieven Clement)
10h00-10h30 BREAK
10h30-12h00 DDA: Hands-on quantification - preprocessing (Lieven Clement)
12h00-13h00 LUNCH
13h00-15h00 DDA: Quantification II - Background on differential analysis and experimental design + Hands-on (Lieven Clement)
15h00-15h30 BREAK
15h30-16h30 DDA: Hands-on quantification of complex designs (Lieven Clement)
16h30-17h30 Visit to the VIB Proteomics core
17h30- Social event
8h15-9h00 Registration and good morning coffee
9h00-9h45 Proteomics applications: N-terminal proteomics (Kris Gevaert)
9h45-10h30 Proteomics applications: multi-omics (Gerben Menschaert)
10h30-11h00 BREAK
12h00-13h00 LUNCH
11h00-11h45 Proteomics applications: AP-MS (Sven Eyckerman)
11h45-12h30 Proteomics applications: Spatial omics (Simon Devos)
12h30-13h30 LUNCH
13h30-14h15 Single cell (Marcel Bühler)
14h15-15h00 Clinical proteomics (Esperanza Fernandez)
15h00-15h30 BREAK
15h30-16h15 Immunopeptidomics (Francis Impens)
16h15-16h30 Concluding remarks
Practical info
26 August 2024 - 30 August 2024
Ghent - Bio-Accelerator Meeting Center
Technologiepark 21
9052 Zwijnaarde
Belgium
26 August 2024 - 30 August 2024
Ghent - Bio-Accelerator Meeting Center
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
26 August 2024 - 30 August 2024
Ghent - Bio-Accelerator Meeting Center
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.
26 August 2024 - 30 August 2024
Ghent - Bio-Accelerator Meeting Center
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 new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.
26 August 2024 - 30 August 2024
Ghent - Bio-Accelerator Meeting Center
+32 9 328 19 02
info@bio-accelerator.com
Ghent-Bio-Accelerator Meeting Center - Marc Van Montagu room