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Proteomics workshop for SciLifeLab bioinformatics community

The aim of this workshop is to present proteomic data to the bioinformatic community at SciLifeLab and thereby enhance networking and collaboration between the bioinformatics and proteomic platforms. The workshop is focused mainly on presenting different proteomic platforms at SciLifeLab in Stockholm and Uppsala as well as describing background and data types in proteomics. The workshop will end with an open discussion about how we can support cross-platform projects. This will hopefully provide a good starting point for synergies between genomics, proteomics and bioinformatics at SciLifeLab.



09:00-09:15 Introducing the workshop and presenting people and aims – Sanela Kjellqvist

09:15-09.30 Protein analysis at SciLifeLab – Janne Lehtiö

09:30-09:45 Wallenberg advanced bioinformatics infrastructure (WABI) – Thomas Svensson

09:45-10:00 Bioinformatics infrastructure for life sciences (BILS) – Bengt Persson

10:00-10:15 Genomics platform SciLifeLab Stockholm – Ellen Sherwood


Proteomics background – basics

10:40-11:00 Introduction about proteins and proteomics – Henrik Johansson

11:00-11.20 Mass spectrometry (MS) data generation – Rui Mamede Branca

11:20-11:40 Protein identification from MS data – Lukas Käll

11:40-12:00 Protein quantifications from MS data – Jenny Forshed

12:00-12:20 Antibody based proteomics – Ulrika Qundos


Facilities at SciLifeLab – Introduction

Core facility service, data generated and bioinformatics bottle necks

13:30-13:50 Biobank profiling facility (Affinity proteomics data) – Mun-Gwan Hong

13:50-14:10 Mass-spectrometry based proteomics platform Uppsala – Jonas Bergquist

14:10-14:30 Advanced mass spectrometry platform Stockholm – Dorothea Rutishauser

14:30-14.50 Proximity ligation assay (PLA) based platform for proteome analyses Uppsala –Masood Kamali-Moghaddam

14:50-15:10 Clinical mass spectrometry facility Stockholm – Lukas Orre


Case studies

15:40-16:00 Aorta proteomics and transcriptomics – Sanela Kjellqvist

16:00-16:20 Genomics and proteomics – Janne Lehtiö


16:20-17:00 How do we support cross platform projects?


For people outside SciLifeLab you will be welcomed by the organizers at the SciLifeLab reception desk at 8.50 and let into the lunch room, floor 2.


Wallenberg Advanced Bioinformatics Infrastructure (WABI) and Clinical Mass Spectrometry

For more information contact: Sanela Kjellqvist