BePa@VIB Proteomics Summer School

BePa@VIB Proteomics Summer School

26 August 2024 - 30 August 2024

Ghent - Bio-Accelerator Meeting Center

omics
live training

BePa@VIB Proteomics Summer School

Target Audience:
VIB PhD student
VIB postdoc
VIB staff scientist
VIB group leader or expert
VIB technical support
Flemish academic or researcher
Non-Flemish academic or researcher
Location:

Ghent - Bio-Accelerator Meeting Center

Duration:

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 !

Learning outcomes

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
VIB Proteomics Core, BE

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. 

Contact An Staes :
Daria Fijalkowska
VIB-UGent Center for Medical Biotechnology, BE

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.

Contact Daria Fijalkowska :
Enrico Massignani
EnricoOK
VIB-UGent Center for Medical Biotechnology, BE

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.

Contact Enrico Massignani :
Francis Impens
VIB Training & Conferences - Trainer picture - Francis Impens
VIB Proteomics Core, BE

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.

Contact Francis Impens :
Gerben Menschaert
University of Ghent, BioBix lab, BE

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
VIB Training & Conferences - Trainer picture - Kris Gevaert
VIB Center for Medical Biotechnology, BE

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.

Contact Kris Gevaert :
Lieven Clement
Lieven
Ghent University, BE

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.

Contact Lieven Clement :
Maarten Dhaenens
UGent ProGenTomics. BE

Dr. Maarten Dhaenens is Executive PI at ProGenTomics (Lab of Pharmaceutical Biotechnology) and President of the Belgian Proteomics Association

Contact Maarten Dhaenens :
Marcel Bühler
Buehler
VIB Center for Medical Biotechnology, BE

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.

Contact Marcel Bühler :
Simon Devos
Simon
VIB Proteomics Core, BE

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.

Contact Simon Devos :
Sven Eyckerman
VIB Training & Conferences - Trainer picture - Sven Eyckerman
VIB-UGent Center for Medical Biotechnology, BE

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
VIB CompOmics group, BE

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.

Contact Tine Claeys :

Program

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

Location & Venue

26 August 2024 - 30 August 2024

Ghent - Bio-Accelerator Meeting Center

Technologiepark 21
9052 Zwijnaarde
Belgium

Public transport

26 August 2024 - 30 August 2024

Ghent - Bio-Accelerator Meeting Center
Public transport

From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.

 

Bike

26 August 2024 - 30 August 2024

Ghent - Bio-Accelerator Meeting Center
Bike

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.

Route description

26 August 2024 - 30 August 2024

Ghent - Bio-Accelerator Meeting Center
Parking

Route description

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.

Venue contact

26 August 2024 - 30 August 2024

Ghent - Bio-Accelerator Meeting Center
Location contact

+32 9 328 19 02

info@bio-accelerator.com

Extra information

Ghent-Bio-Accelerator Meeting Center - Marc Van Montagu room