BePa@VIB International Proteomics Summer School
5 days
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 organised with the support of the Flemish Government.
The workshop 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.
Christine Carapito
Christine Carapito is a Research Director at CNRS and University of Strasbourg and a group leader at the Hubert Curien Pluridisciplinary Institute in France. Her research focuses on quantitative mass spectrometry methods development and their application to a wide range of biological questions.
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 Group Leader at the VIB Center for Medical Biotechnology.
Lennart Martens
Dr. Lennart Martens is Senior Full Professor of Systems Biology at Ghent University, and Group Leader at the VIB Center for Medical Biotechnology. His research focuses on advanced (machine learning) algorithms for proteomics data interpretation and exploration.
Lieven Clement
Lieven Clement is 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
Nikolai Slavov
Nikolai Slavov received undergraduate education at MIT and pursued doctoral research in the Botstein laboratory at Princeton University, aiming to understand how cells coordinate growth rate, gene expression, and metabolism. During his postdoctoral research in the van Oudenaarden laboratory at MIT, he characterized trade-offs of aerobic glycolysis (also known as Warburg effect). His laboratory explores the functional roles of ribosome heterogeneity and the regulation of protein synthesis in single cells. Most recently, the Slavov laboratory developed high-throughput technologies for single-cell proteomics by mass-spectrometry and is applying them to quantify post-transcriptional regulation in complex diverse biological systems. Professor Slavov is a recipient of an NIH Director's Award and an Allen Distinguished Investigator Award.
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.
Program
- Day 1: Sample preparation
- Day 2: Data acquisition
- Day 3: International speaker
- Day 4: Identification
- Day 5: Quantification
8h00-8h45 Registration and good morning coffee
8h45-9h00 Welcome (Maarten Dhaenens)
9h00-10h00 Proteomics applications: an overview (An Staes, Kris Gevaert, Gerben Menschaert, Sven Eyckerman)
10h00-10h30 BREAK
10h30-12h00 Proteomics applications: an overview (An Staes, Kris Gevaert, Gerben Menschaert, Sven Eyckerman)
12h00-13h00 LUNCH
13h00-14h00 Sample preparation PART 1: do's and don'ts (An Staes)
14h00-15h00 Flash presentation (1min/person)
15h00-15h30 BREAK
15h30-16h45 Sample preparation PART 2: do's and don'ts (Kris Gevaert)
16h45-17h30 Q&A session
8h00-8h45 Registration and good morning coffee
8h45-10h00 Shotgun 1: Data dependent acquisition: the basics and instrument design (An Staes)
10h00-10h30 BREAK
10h30-12h00 Visit to the VIB Proteomics core
12h00-13h00 LUNCH
13h00-15h00 Shotgun 2: Data Independent acquisition: the basics (Maarten Dhaenens)
15h00-15h30 BREAK
15h30-17h30 Other acquisitions and targeted proteomics (An Staes)
9h00-10h30 Christine Carapito: An MS trip to where the very small matters very much
10h30-12h30 DIA: Data structure and analysis (Maarten Dhaenens)
12h30-13h30 LUNCH
13h30-17h30 Social event: walk through Ghent and visit to brewery Gruut
8h00-8h45 Registration and good morning coffee
8h45-10h00 DDA: The theory of identification (Lennart Martens, Lieven Clement)
10h00-10h30 BREAK
10h30-12h00 DDA ID: practical
12h00-13h00 LUNCH
13h00-14h00 DDA ID: practical ctd
14h00-15h00 Q&A session
15h00-15h30 BREAK
15h30-17h00 Nikolai Slavov: Biological and technological frontiers for single-cell proteomics
8h00-8h45 Registration and good morning coffee
8h45-10h00 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
15h30-16h15 DDA: Hands-on quantification of complex designs (Lieven Clement)
16h15-17h00 Overall Q&A
17h00-17h30 Concluding remarks
Practical info
28 August 2023 - 29 August 2023
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
30 August 2023
Ghent - Clemenspoort
Overwale 3
9000 Ghent
Belgium
31 August 2023 - 01 September 2023
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
28 August 2023 - 29 August 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.
30 August 2023
Ghent - Clemenspoort
The train station Ghent St-Pieters is only 250 m away. We have 40 bike lots.
31 August 2023 - 01 September 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.
28 August 2023 - 29 August 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).
30 August 2023
Ghent - Clemenspoort
We offer parking lots (1.20 € per hour). GPS address: Sint-Denijslaan 251.
Please take the neem the exit SPORTHAL HoGent (not Campus HoGent) and drive all the way to the end, so past the parking slots of HoGent.
31 August 2023 - 01 September 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).
28 August 2023 - 29 August 2023
Ghent - VIB/UGent FSVM II
30 August 2023
Ghent - Clemenspoort
+32 476 46 10 40