Course
Advanced Proteomics
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
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. For the first time participants will use the new MS called Orbitrap HF-X.
In this course the focus will be on sample preparation and data analysis.
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.
Course aim
Participants will learn
- how to make state of the art proteomics samples
- perform proteomic data analysis using MaxQuant
- integrate results into biological research
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 days hands-on course with a maximum of 16 participants (PhD’s and postdocs are the focus group). In the morning sessions lectures on mass spectrometry and proteomics applications and in the afternoon sessions practical work are 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 the newest MS: Q-Exactive HF-X. See gel criteria.
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Gel criteria
During the course, all participants will do their own in-gel digestion on their own sample and, when the nLCMSMS measurement has been done for you, analyse their own results. Every participant can have one nLCMS(MS) run being done.
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 a week before start of the course. In this case, send 50 ng or more of lyophilized protein sample
before 1 August 2019 to:
Sjef Boeren
Biochemistry
Stippeneng 4
6708 WE Wageningen
The Netherlands.
Please do not send any potentially toxic or otherwise harmful materials to our lab. We have no facilities to handle those at all.
Organisation
Course coordinators
Laboratory of Biochemistry, Wageningen University & Research, The Netherlands
- Prof Jacques Vervoort
- Sjef Boeren
Speakers
- Dr. Guido Hooiveld - Division of Human Nutrition and Health, Wageningen University & Research, The Netherlands
- Dr. Tami Geiger - Tel Aviv University, Israel
- Dr. Maarten Altelaar - Netherlands Proteomics Centre, The Netherlands
Date & duration & language
The Masterclass will be held from 27 August - 30 August 2019. The course will be conducted in English.
Study load
The study load of this masterclass is 1.4 ECTS = 39 hours.
Contact information
Information concerning the course contents can be obtained from Prof. Jacques Vervoort
For organisational matters please contact:
Mrs. Cornelia van Bree-Evers
Location & accommodation
Lectures and practicals will be given at Wageningen University & Research
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.
A number of hotel rooms have been blocked at the Wageningen International Congress Centre (WICC). Accommodation costs are €69,- (single room, inlc. breakfast) per night. Participants have to book their own room by sending an e-mail to: info@wicc.nl Please book your room before 28 June 2019 and mention booking code 'Pro19'.
Registration & course fee
To register please complete the electronic reply form before 28 June 2019
The number of participants to the course is limited to 16.
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 (cornelia.vanbree-evers@wur.nl) before 9 July 2019.
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:
| Bring own gel | Have gel ran | |
| WUR PhD candidates | € 300 | € 325 |
| All other PhD candidates/Postdoc & staff from VLAG | € 550 | € 575 |
| University staff / Non-Profit | € 775 | € 825 |
| Industry / For-Profit | € 1650 | € 1825 |
Cancellations policy
No charge until 1 July 2019
25% of the course fee paid or due till 1 August 2019
No refund after 1 August 2019
Substitutions for participants may be made at any time until 12 August 2019