Course
Advanced Proteomics 8th edition
Proteomics is the study of the proteome, the set of proteins expressed in an organism. The proteome can change dramatically depending on biological conditions. Proteomics is able to capture detailed snapshots of the proteome using mass spectrometry. The rapid development in technical advances of instrumentation has led to new bioinformatics approaches. In this course the focus will be on sample preparation and data analysis.
Background
Mass spectrometry (MS)-based proteomics is the most comprehensive approach for the quantitative profiling of proteins, their interactions, and modifications. Proteomics is the study of the proteome, the set of proteins expressed in an organism. The proteome can change dramatically depending on developmental stage, biological conditions, and subcellular localisation. Proteomics is able to capture detailed snapshots of the proteome using mass spectrometry. The rapid development in technical advances of instrumentation has led to new bioinformatics approaches. In this course the focus will be on sample preparation, data analysis, and new methods in MS-based proteomics approaches.
Aim
Participants will learn;
- how to make a proteomics sample
- perform proteomic data analysis using MaxQuant
- integrate results into biological research.
Target group
PhD candidates or Postdocs interested in this course should work on proteomics projects or plan to use proteomics in the near future and have a strong background in nutrition, biochemistry, physiology, molecular biology or a comparable discipline.
Programme topics
- Sample preparation protocols
- Proteomics instrumentation
- Quantitative techniques
- MaxQuant and Perseus
- Integration of ~omics data
- New mass spectrometric tools in proteomics
Course format
The course is a 4-day long hands-on course with a maximum of 25 participants.
We will schedule lectures on mass spectrometry and proteomics applications in the morning sessions and in the afternoon sessions practical work is scheduled. Each participant can bring their own sample as one slice or spot of a SDS protein 1 or 2D gel. Samples will be prepared by the participants and measured using splitless nano-LC Orbitrap FTMSMS.
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Gel criteria
During the course, all participants will do their own in-gel digestion on their own sample. The nLCMSMS measurement will be done by our MS specialist and afterward participants will analyse their own results.
When you can and want to run a protein SDS-gel in your own lab, then stain it with either Coomassie or Oriole and cut out a gel band or slice smaller than 1 cm2. Please do not use cross-linking agents like glutaraldehyde or formaldehyde. The gel bands or slice can be taken along in an Eppendorf tube with some liquid (5% acetic acid / 45% water / 50% methanol) added to it.
For those people who do not have the facilities to run a protein SDS-gel in their own lab, we offer to have a protein gel ran in our lab in Wageningen together with you one day before start of the course. Please do not bring any potentially toxic or otherwise harmful materials to our lab. We have no facilities to handle those.
Organisation
Course coordinators
- Elwira Smakowska-Luzan, Laboratory of Biochemistry, Wageningen University and Research
- Sjef Boeren, Laboratory of Biochemistry, Wageningen University and Research
Other faculty
- Prof. Maarten Altelaar - Netherlands Proteomics Centre, The Netherlands
- Dr Carlo De Nart - Max Planck Institute of Biochemistry, Germany
- Dr Juan Luis Restrepo Lopez - Max Planck Institute of Biochemistry, Germany
- Dr Maria Suarez Diez - Laboratory of Systems and Synthetic Biology, Wageningen University and Research
- Dr Mark Roosjen - Laboratory of Biochemistry, Wageningen University and Research
Date & duration & language
The course will be held from 7 - 10 February 2023 (4 days). The course will be conducted in English.
Study load
The study load of this masterclass is 1.4 ECTS
Contact information
Information concerning the course contents can be obtained from Dr Elwira Smakowska-Luzan
For organisational matters please contact: Cornelia van Bree-Evers
Location & accommodation
Lectures and practicals will be given at Wageningen University & Research, Wageningen, the Netherlands.
The town of Wageningen is 5 km from Ede-Wageningen railway station, with transport options being taxi or bus. Ede-Wageningen railway station is about one and a half hours from Amsterdam Schiphol Airport. For train schedules visit: www.ns.nl.
Suggestion for accommodations in Wageningen listed below:
Hotels:
Other accomodation:
Registration & course fee
The course is fully booked. If you would like to be placed on the waiting list (in case of cancellations), please send an e-mail to Cornelia van Bree.
The number of participants to the course is limited to max. 25.
In view of the limited number of participants, PhD candidates and postdocs applying will be selected. Each participant should therefore indicate in 1/2 A4 (maximum) the background of her/his project. Information about the background of your project should be sent to Cornelia van Bree-Evers no later than 20 November, also indicate whether you will bring a gel piece or if you want to have it run in Wageningen on Monday 6 February!. You will be informed before 8 December at the latest if you get selected or not.
Course fee
Course fee includes course material, practical work, coffee/tea during breaks, lunches and one dinner but does not cover accommodation. The course fee depends on the participant's affiliation:
| WUR PhD candidates affiliated with VLAG/EPS/WIMEK/WASS/WIAS/PE&RC | € 275 |
| All other PhD candidates/Postdoc & staff from VLAG | € 500 |
| University staff / Non-Profit | € 725 |
| Industry / For-Profit | € 1600 |