Mass spectrometry data processing
General context
Please watch the video playlist by Lennart Martens in preparation for the training: https://www.youtube.com/playlist?list=PLXxp6nsBenSX_W8DiOocKJ0laNauYNdYl
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 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.
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 (LC)
10u15-11u15: Tutorial 2.3: Impact of different summarization 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
21 April 2022 - 22 April 2022
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
21 April 2022 - 22 April 2022
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
21 April 2022 - 22 April 2022
Ghent - VIB/UGent FSVM II
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.
21 April 2022 - 22 April 2022
Ghent - VIB/UGent FSVM II
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 parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.