Location & dates EMBL Heidelberg, Germany 5 - 10 May 2019
Deadlines Application closed
organiser_EMBO_Course_2017

Programme

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Day 1 - Sunday 5 May 2019
TimeSpeakerLocation
13:45 - 14:00

Arrival & Welcome

Computer Training Lab

14:00 - 14:45

Introduction: Quantitative proteomics for biology
Jeroen Krijgsveld  - DKFZ, Heidelberg, Germany
Paola Picotti - ETH Zurich, Switzerland
Misha Savitski - EMBL Heidelberg, Germany

Computer Training Lab

14:45 - 16:15

Lecture: Peptide chromatography in proteomics
Shabaz Mohammed - University of Oxford, UK

Computer Training Lab
16:15 - 16:30

Coffee break

Computer Training Lab

16:30 - 17:30

Flash talks by participants - Even numbers

Computer Training Lab

17:30 - 18:30

Poster session (even numbers) & Drinks

Operon Foyer

18:30

Dinner

Operon Foyer

Day 2 - Monday 6 May 2019
TimeSpeakerLocation
09:00 - 10:00

Lecture: MS technologies
Dominic Helm - EMBL Heidelberg, Germany

Computer Training Lab

10:00 - 11:15

Lecture: Protein identification
Lennart Martens - University of Ghent, Belgium

Computer Training Lab

11:15 - 11:30

Coffee break

Computer Training Lab

11:30 - 12:30

Practical: Protein identification
Lennart Martens - University of Ghent, Belgium
Tim Van Den Bossche - University of Ghent, Belgium

Computer Training Lab

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 15:00

Practical: Peptide and Protein Identification
Lennart Martens - University of Ghent, Belgium
Tim Van Den Bossche - University of Ghent, Belgium

Computer Training Lab

15:00 - 16:15

Lab tour + Coffee break

Computer Training Lab

16:15 - 17:00

Flash talks by participants - Odd numbers

Computer Training Lab

17:00 - 18:00

Lecture: Application talk
Paola Picotti - ETH Zurich, Switzerland

Computer Training Lab

18:00 - 19:00 Dinner

EMBL Canteen

19:00 - 20:00

Poster session (Odd numbers) & Drinks

Operon Foyer

Day 3 - Tuesday 7 May 2019
TimeSpeakerLocation
09:00 - 10:00

Lecture: MS1-based quantification
Moritz Janda - Thermo Fisher Scientific, Germany

Computer Training Lab

10:00 - 12:30

Practical: Data analysis by MaxQuant
Juergen Cox - Max Planck Institute, Germany

Computer Training Lab

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 15:30

Practical: Data analysis by MaxQuant
Juergen Cox - Max Planck Institute, Germany

Computer Training Lab

15:30 - 16:00

Coffee break

Computer Training Lab

16:00 - 17:00

Lecture: Application talk ‘Data integration’
Jyoti Choudhary - The Institute of Cancer Research, UK

Computer Training Lab

17:00 - 18:00

Lecture: Application talk ‘Proteome dynamics’
Jeroen Krijgsveld - DKFZ, Germany

Computer Training Lab

18:00 - 19:00 BBQ Dinner

ISG Hotel

Day 4 - Wednesday 8 May 2019
TimeSpeakerLocation
09:00 - 10:30

Lecture: Introduction and application talk MS2-based quantification: TMT
Misha Savitski - EMBL Heidelberg, Germany

Computer Training Lab

10:30 - 12:00

Practical: Statistical analysis of quantitative proteomics data
Misha Savitski - EMBL Heidelberg, Germany
Frank Stein - EMBL Heidelberg, Germany
Nils Kurzawa - EMBL Heidelberg, Germany

Computer Training Lab

12:00 - 13:00

Lunch break

EMBL Canteen

13:00 - 14:30

Practical: Statistical analysis of quantitative proteomics data
Misha Savitski - EMBL Heidelberg, Germany
Frank Stein - EMBL Heidelberg, Germany
Nils Kurzawa - EMBL Heidelberg, Germany

Computer Training Lab

14:30 - 14:45

Coffee break

Computer Training Lab

14:45 - 17:30

Introduction and tutorial: ‘Label-free quantification & MS platforms for DDA and DIA’
Moritz Janda - Thermo Fisher Scientific, Germany

Computer Training Lab

17:30

Free evening

Day 5 - Thursday 9 May 2019
TimeSpeakerLocation
09:00 - 10:30

Targeting proteomes using data independent acquisition (DIA)-based proteomics and SWATH-MS - An introduction into the basic principles
Christina Ludwig - Technical University Munich, Germany

Computer Training Lab

10:30 - 11:00

Coffee break

Computer Training Lab

11:00 - 12:30

Life demonstration (practical session): “An introduction into Skyline – a chromatogram-based software tool for targeted proteomics”
Christina Ludwig - Technical University Munich, Germany
Monika Pepelnjak - ETH Zürich, Switzerland

Computer Training Lab

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 16:00

Tutorial (practical session): “Label-free quantification of DIA/SWATH data using Skyline”
Christina Ludwig - Technical University Munich, Germany
Monika Pepelnjak - ETH Zürich, Switzerland

Computer Training Lab

16:00 - 17:00

Lecture: 'Cross-linking mass spectrometry’
Fan Liu - Leibniz Institute for Molecular Pharmacology, Germany

Computer Training Lab

17:00 Guided City Tour & Dinner Downtown

Day 6 - Friday 10 May 2019
TimeSpeakerLocation
09:00 - 10:00

Lecture: Methods for Whole Proteoform Characterization and Quantitation
Neil Kelleher - Northwestern University, USA

Computer Training Lab

10:00 - 12:30 Break-out session: discussion groups

Computer Training Lab

12:30 - 13:30 Lunch break

EMBL Canteen

13:30 - 14:30

Presentations from break-out session & panel discussion

Computer Training Lab

14:30 - 15:30

Lecture: 'Spatial proteomics'
Kathryn Lilley - Cambridge University, UK

Computer Training Lab

15:30 - 16:00 Recap & farewell

Computer Training Lab

16:00

Bus to Heidelberg Train Station & Crown Plaza Hotel