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Quantitative Proteomics: Strategies and Tools to Probe Biology – Course and Conference Office

EMBO Practical Course

Quantitative Proteomics: Strategies and Tools to Probe Biology

Overview

EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.

Course Overview

This course will provide both theoretical and practical training in the use of quantitative proteomics approaches.  Participants will learn the principles of current methodologies including label-free, SILAC and TMT as well as targeted proteomics, and they will be trained in the use of bioinformatic tools for data analysis. 

Audience

This course is aimed at researchers who know the basics of proteomics and who want to get a deeper understanding of quantitative methodologies, and at those who are familiar with wet-lab proteomic experimentation but want to gain experience in bioinformatic data interpretation. To enter the course a basic understanding of mass spectrometry-based proteomics is beneficial.

Modules/Resources

  • The principles of proteome quantification by stable isotope labeling (SILAC and TMT), label-free, and targeted proteomics
  • Introduction how various types of mass spectrometers can be used for proteome quantification
  • Computer training sessions using software tools for the analysis of various quantitative proteomic data types
  • Lectures demonstrating the application of quantitative proteomics in biology, clinical research and drug discovery

Learning Outcomes

  • Understand the principles and use cases of quantitative proteomic methods
  • Ability to design quantitative proteomic experiments, including selection of the most appropriate hardware and software
  • Ability to analyse quantitative proteomic data by various software tools

What past participants say about the course:

“This course aids you in paving the way towards the full potential of quantitative proteomics and is essential for both new and experienced users.” — Jarne Pauwels, VIB-University Ghent.

“I enthusiastically highly recommend this course to anyone interested in quantitative MS. The high caliber of speakers, combination of theoretical with practical applications, organization and international participants made this an especially wonderful academic experience.” — Enzo Scifo, Campbell Family Mental Health Research Institute of CAMH, University of Toronto, Canada.

Speakers and Trainers

Scientific Organisers

Course Organisers

Irena Provaznikova

EMBL Heidelberg, Germany

Programme

Got something to say? Tweet it with #EMBOQuantPro 

  • The virtual course will start on Monday 26 April with an onboarding session and access to the pre-recorded talks from invited speakers and trainers. The course will continue on Monday 3 May with the regular programme.
  • Participants will be required to view the pre-recorded talks (7 h) prior to the main start of the course on Monday 3 May. During the five-day course duration, full-time attendance is required.  

The following times are used in the programme below:

  • Central European Time (CEST): eg. Berlin, Amsterdam Paris
  • Eastern Standard Time (EDT): eg. New York, Quebec

To find out the equivalent time zone in your location, enter Berlin, the CEST programme time and your city into the Time Zone Converter.

Day 0 – Monday 26 April 2021
Time (EDT)Time (CEST)Speaker
04:00-05:3010:00-11:30
Onboarding and technical troubleshooting (optional)
Day 1 – Monday 3 May 2021
Time (EDT)Time (CEST)Speaker
03:30-03:45 09:30-09:45
Welcome and Introduction by organisers
Jeroen Krijgsveld  – German Cancer Research Center, Germany
Christina Ludwig – Technical University Munich, Germany
Mikhail Savitski – EMBL Heidelberg, Germany
03:45-05:0009:45-11:00

Interactive: Icebreaker 
05:00-05:15 11:00-11:15
Coffee break
05:15-06:00 11:15-12:00
Panel discussion based on the pre-recorded talks: 
LC & MS Technologies, Protein Identification
 
Dominic Helm – German Cancer Research Center, Germany  
Shabaz Mohammed – University of Oxford, UK
Lennart Martens – Ghent University, Belgium 
Mandy Rettel – EMBL Heidelberg, Germany
06:00-07:00 12:00-13:00
Lunch break
07:00-09:00 13:00-15:00
Practical: Protein identification 
Lennart Martens – Ghent University, Belgium 
Tim Van Den Bossche – Ghent University, Belgium
09:00-09:15 15:00-15:15
Coffee break
09:15-09:45 15:15-15:45
Virtual Social Programme: Speed networking
Day 2 – Tuesday 4 May 2021
Time (EDT) Time (CEST) Speaker
04:00-04:05 10:00-10:05
Overview of the day 
04:05-04:50 10:05-10:50
Application talk: Phosphoproteomics
Judit Villén – University of Washington, USA 
04:50-05:00 10:50-11:00
Coffee break
05:00-05:30 11:00-11:30
Live recap and Q&A based on the pre-recorded talk:
Open search PTM analysis
Alexey Nesvizhskii – University of Michigan, USA
05:30-06:00 11:30-12:00
Practical session: Open search strategy
for PTM analysis
Alexey Nesvizhskii – University of Michigan, USA
06:00-07:00 12:00-13:00
Lunch break
07:00-09:00 13:00-15:00
Practical session: Open search strategy
for PTM analysis
Alexey Nesvizhskii – University of Michigan, USA 
09:00-09:30 15:00-15:30
Virtual Social Programme: Quiz
Day 3 – Wednesday 5 May 2021
Time (EDT) Time (CEST) Speaker
04:00-04:05 10:00-10:05
Overview of the day 
04:05-04:50 10:05-10:50
Live recap and Q&A: DIA/SWATH 
Christina Ludwig – Technical University Munich, Germany
Miriam Abele – Technical University Munich, Germany 
Julia Mergner- Technical University Munich, Germany 
04:50-05:00 10:50-11:00
Coffee break
05:00-06:00 11:00-12:00
Practical: Label-free quantification by DIA using Skyline
Christina Ludwig – Technical University Munich, Germany
Miriam Abele – Technical University Munich, Germany 
Julia Mergner- Technical University Munich, Germany 
06:00-07:00 12:00-13:00
Lunch break
07:00-09:00 13:00-15:00
Practical: Label-free quantification by DIA using Skyline
Christina Ludwig – Technical University Munich, Germany
Miriam Abele – Technical University Munich, Germany 
Julia Mergner- Technical University Munich, Germany 
09:00-09:45 15:00-15:45
Preparation of the group challenges by participants
Day 4 – Thursday 6 May 2021
Time (EDT) Time (CEST) Speaker
04:00-04:05 10:00-10:05
Overview of the day 
04:05-04:20 10:05-10:20
Homework check from the practical session:
Label-free quantification by DIA/SWATH using
Christina Ludwig – Technical University Munich, Germany
04:20-04:50 10:20-10:50
Panel discussion based on the pre-recorded talks:
Quantification and proteome dynamics
Jeroen Krijgsveld  – German Cancer Research
Center, Germany
Christina Ludwig – Technical University Munich, Germany
Mikhail Savitski – EMBL Heidelberg, Germany
04:50-05:00 10:50-11:00
Coffee break
05:00-06:00 11:00-12:00
Interactive session:
Challenges in proteomics – ask the expert
Jeroen Krijgsveld  – German Cancer Research
Center, Germany
Christina Ludwig – Technical University Munich, Germany
Mikhail Savitski – EMBL Heidelberg, Germany
Simone Sidoli – Albert Einstein College of Medicine, USA
06:00-07:00 12:00-13:00
Lunch break
07:00-07:45 13:00-13:45
Application talk: Histone PTMs
Simone Sidoli – Albert Einstein College of Medicine, USA
07:45-08:30 13:45-14:30
Application talk: MS of intact proteins
Michal Sharon – Weizmann Institute of Science, Israel
08:30-08:45 14:30-14:45
Coffee break 
08:45-09:15 14:45-15:15
Panel discussion:
Posttranslational Modifications in Proteomics
Simone Sidoli – Albert Einstein College of Medicine, USA
Judit Villén – University of Washington, USA 
09:15-09:30 15:15-15:30
Coffee break
09:30-10:00 15:30-16:00
Virtual Social Programme: Bar Mixer
Day 5 – Friday 7 May 2021
Time (EDT) Time (CEST) Speaker
04:00-04:05 10:00-10:05
Overview of the day
04:05-04:50 10:05-10:50
Application talk: Proteomics in basic
and translational research
Ruedi Aebersold – ETH Zürich, Switzerland 
04:50-05:00 10:50-11:00
Coffee break
05:00-06:00 11:00-12:00
Open discussion
Ruedi Aebersold – ETH Zürich, Switzerland
06:00-07:00 12:00-13:00
Lunch break
07:00-08:15 13:00-14:15
Presentation of the group challenges
by participants 
08:15-09:00 14:15-15:00
Summary of the course and virtual farewell (group photo)
09:0015:00
End of course

Practical Information

Registration Fees and Motivation Letter

Registration Fees and Motivation Letter

The course is limited to 24 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration Fees (include admission, course materials):

Academia125 Euro
PhD Student125 Euro
Industry225 Euro

Confirmation and Payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation Letter Submission

After registration, you can submit your motivation letter via a separate link that will be provided in the email confirmation. Alternatively, you can access the link on the confirmation page directly after registering. The same login credentials are used for both processes.

Guidelines

  1. Select your account as the author of the submission.
  2. When describing your motivation to apply for the course, include your relevant skills, experience and qualifications showing why you would be suitable for the course. In addition, explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.
  3. You may be asked to answer the following questions, as well as questions about your experience with various techniques and methods.
  • What was/is your undergraduate degree?
  • What was/is your postgraduate degree?
  • What was/is the title and focus of your postgraduate degree thesis?
  • Please describe your research.
  • Please list the scientific positions in which you have been employed in your career so far
  • Please list if you have received any awards during your research.
  • Please list any papers you have published.
  • What is your expectation from this course?

Please note:

Motivation letter length: 
The maximum limit of 2000 characters refers to manually typed text (spaces included).

Additional questions: The maximum characters for your answers in the free text field boxes is 255 (spaces included).

Text only:
 If you copy-paste the text, hidden formatting might still be included and you will be informed that your text exceeds the character limit. We recommend either:

  1. saving your text as text only in your editor or Email programme, OR
  2. copy-pasting it into Notepad and then onto the website.


Symbols: 
If you have special symbols in your text make sure you are using Unicode characters, otherwise these will not be recognised by the tool.

Further Details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants 

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. In order to apply for this grant, you must be registered by the abstract submission deadline.

Boehringer Ingelheim Fonds Travel Grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance to the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal by following the instructions here. Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

*For some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.

Selection

The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

A list of external funding opportunities can be found here, and information on attending a conference as an event reporter here.

For further information about financial assistance please refer to the FAQ page.

Sponsors

Sponsorship Opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Date: 3 - 7 May 2021

Location: Virtual


Deadline(s):

Registration: Closed


Contact: Raili Pall


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

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