Course
Advanced proteomics
Learning how to make state of the art proteomics samples, performing proteomic data analysis using MaxQuant and integration of results into biological research
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 techniques. 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.
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.
Course design
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 splitless nano-LC LTQ Orbitrap XL FTMSMS.
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 2 weeks before the course starts to: Sjef Boeren, Biochemistry, Stippeneng 4, 6708 WE Wageningen. Please do not send any potentially toxic or otherwise harmful materials to our lab. We have no facilities to handle those at all.
Programme topics
- Sample preparation protocols
- Proteomics instrumentation
- Quantitative techniques
- MaxQuant and Perseus
- Integration of ~omics data
- New mass spectrometric tools in proteomics
Organisation
Course coordinators
- Prof. Jacques Vervoort, Laboratory of Biochemistry, Wageningen University
- Sjef Boeren, Laboratory of Biochemistry, Wageningen University
Other faculty
- Dr. Tami Geiger, Tel Aviv University, Israel
- Dr. Peter van Baarlen, Wageningen University, The Netherlands
- Dr. Maarten Altelaar, Netherlands Proteomics Centre, The Netherlands
Date & duration
The course will be held from 1 - 4 May 2017 (4 days).
Study load
The study load of this course is 1.4 ECTS credits.
Language
The course language will be English.
Contact information
More information about the course contents can be obtained from:
Prof. Jacques Vervoort
Email: Jacques.Vervoort@wur.nl
For organisational matters please contact:
Mrs. Ingeborg van Leeuwen-Bol
Email: Ingeborg.vanLeeuwen-Bol@wur.nl
Location & accommodation
Lectures will be given at:
Wageningen University,
Axis-Z, Building 118
Bornse Weilanden 9
6708 WG Wageningen
The Netherlands
Wageningen is located 5 kms from the railway station of Ede-Wageningen. The conference centre can be reached by train (railway station Ede-Wageningen) and bus/taxi in less than two hours from Amsterdam Schiphol Airport (see for train schedules: www.ns.nl).
Participants have to book their own hotel room. A number of hotel rooms have been blocked at Hotel de Wageningsche Berg for course participants, but only until 16 March 2017. Accommodation costs are € 85 (double room; incl. breakfast, excl. € 2 Tax) per night. For booking send an email to: info@hoteldewageningscheberg.nl. Mention booking code PRO17.
Registration & course fee
You can register here.
The final registration date is 1 February 2017.
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 Ingeborg van Leeuwen-Bol (Ingeborg.vanLeeuwen-Bol@wur.nl).
| bring own gel | have gel ran | |
|---|---|---|
| PhD candidates affiliated with VLAG | € 275 | € 350 |
| PhD candidates | € 500 | € 575 |
| University staff / Non -Profit | € 750 | € 800 |
| Industry / For-Profit | € 1600 | € 1800 |
The course fee includes course material, practical work, lunches/tea/coffee and one dinner.
Cancellations policy
- No charge until 1 February 2017
- 25% of the course fee paid or due till 1 April 2017
- No refund after 1 April 2017
- Substitutions for participants may be made until 17 April 2017