Mass spectrometry data processing
General context
In this training session we start by reviewing the types of mass spectrometer, and what the properties of their output data are. Out of our understanding of the data, we learn to extract meaningful interpretations.
- Obtain a good understanding of the origins and properties of mass spec data
- Obtain an understanding of the processing of mass spec data, aimed at identifying and quantifying peptides and proteins
- Gain sufficient understanding of the software tools and database used, and of the issues and caveats involved, to critically analyse and assess results from mass spectrometry based proteomics experiments
A basic understanding of mass spectrometry as applied to peptides and proteins is required by the participants.
Trainers
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.
Program
09h30 - 11h00: Search engines (LM)
11h00 - 11h15: Break
11h15 - 12h00: Practical 1.3 - search engines + questions
12h00 - 12h30: Other identification strategies
12h30 - 13h30: Lunch
13h30 - 14h30: Identification reliability and protein inference
14h30 - 15h15: practical 1.4 & 1.5: identification reliability and protein inference
15h15 - 15h30: Break
15h30 - 16h00: MS1 Quantification with moFF
16h00 - 17h00: Practical: moFF
9u30-10u15: Preprocessing & Differential Analysis of experiments with simple designs
10u15-11u15: Tutorial 2.3: Impact of different summarisation methods
11u15-11u30: Break
11u30-12u30: Tutorial 2.4 - Tutorial 2.5
12u30-13u30: Lunch
13u30-14u30: Statistical Inference & Analysis of Experiments with Factorial Designs
14u30-15u30: Tutorial 3.3: Impact of Blocking
15u30-15u45: Break
15u45 - 16u30: Tutorial 3.4: Statistical inference for experiments with multiple factors
16u30 - 17u00: Wrap-up and Questions
Practical info
Ghent - iGent
Technologiepark-Zwijnaarde 126
9052 Gent
Belgium
Ghent - iGent
Several buses drive between Gent Sint-Pieters railway station and Technologiepark: Bus 70, 71 and 72 (‘Tramstraat’)
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Get off at the stop marked 'Bollebergen' at Grote Steenweg Noord.
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Technologiepark is straight in front of you on the other side of the soft verge.
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Walk into the park to the roundabout. You can see the iGent Tower on your left.
Shuttle bus
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The shuttle service between Gent Sint-Pieters and Technologiepark runs every 15 minutes during peak hours (7.30 - 9.30 am and 4.30 - 6.30 pm).
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The site has four stops, including one nearly in front of the iGent Tower (4th stop).
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More info on the Tech Lane Ghent Science Park site.
Ghent - iGent
You can park your car on the Tech Lane Ghent Science park in the open car parks (no barriers), like the one in front of the iGent tower across the road. These car parks have Dutch signs which read "Parkeren uitsluitend met vignet! (overtreding = wielklem)”. This means you should only park there if you have a valid car park permit. You can request such a permit by sending an email to your contact person at iGent. The permit is only valid for a single day, and will need to be placed visibly behind the car's windscreen.