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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

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

Course overview

This course will provide both theoretical and practical training in the use of quantitative proteomics. Participants will learn the principles of the most frequently used data acquisition methods (DDA, DIA, and targeted proteomics) and proteomic quantification approaches (label-free, SILAC, and TMT). The major aim of this course is to practically train the participants in the use of readily available bioinformatic tools as well as in the statistical interpretation of proteomic data, in order to empower them to make informed decisions in their own research.

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

Speakers

Speakers, trainers, and staff

Fan Liu

Leibniz-Forschungsinstitut für Molekulare Pharmakologie

Germany

Scientific organisers

Course organisers

Aline Schnieder

Course and Conference Officer

EMBL Heidelberg

Germany

Swetlana Krez

Training Lab Technician

EMBL Heidelberg

Germany

Programme

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  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Sunday, 11 June 2023
Time (Europe/Berlin)SessionLocation
13:00Bus to EMBL ATCISG Hotel
13:30 – 14:00Registration, welcome and housenotesCourtyard Room A & B
14:00 – 14:45Introduction: Quantitative proteomics for biology
Jeroen Krijgsveld – German Cancer Research Center (DKFZ)/University of Heidelberg, Germany
Christina Ludwig – Technical University Munich, Germany
Mikhail Savitski – EMBL Heidelberg, Germany
Courtyard Room A & B
14:45 – 16:00Lecture: Peptide chromatography in proteomics (remote lecture)
Shabaz Mohammed – University of Oxford, UK
Courtyard Room A & B
16:00 – 16:30Coffee BreakCourtyard Room A & B
16:30 – 17:30Flash talks 1 (odd numbers)Courtyard Room A & B
17:30 – 19:00Poster Session (odd numbers) with drinks and snacksHelix B
19:00 – 20:00DinnerEMBL Canteen
20:00Bus to ISG HotelATC entrance
Day 2 – Monday, 12 June 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:05Overview of the dayCourtyard Room A & B
09:05 – 10:05Lecture: MS technologies
Dominic Helm – German Cancer Research Center (DKFZ), Germany
Courtyard Room A & B
10:05 – 11:20Lecture: Peptide and protein identification
Lennart Martens – Ghent University, Belgium
Courtyard Room A & B
11:20 – 11:35Coffee BreakCourtyard Room A & B
11:35 – 12:35Practical session 1: Peptide and protein identification
Lennart Martens – Ghent University, Belgium
Miriam Abele – Technical University Munich, Germany
Tine Claeys – Ghent University, Belgium
Christina Ludwig – Technical University Munich, Germany
Julia Mergner – Technical University Munich, Germany
Computer Training Lab
12:35 – 13:35LunchEMBL Canteen
13:35 – 15:05Practical session 1 (cont.): Peptide and protein identification
Lennart Martens – Ghent University, Belgium
Miriam Abele – Technical University Munich, Germany
Tine Claeys – Ghent University, Belgium
Christina Ludwig – Technical University Munich, Germany
Julia Mergner – Technical University Munich, Germany
Computer Training Lab
15:05 – 16:20Coffee break and Lab tourCourtyard Room A & B / Proteomics Core Facility
16:20 – 17:20Flash talks 2 (even numbers)Courtyard Room A & B
17:20 – 18:20Application talk 1: Cancer proteogenomics
Janne Lehtiö – Karolinska Institute, Sweden
Courtyard Room A & B
18:20 – 19:20DinnerEMBL Canteen
19:20 – 20:50Poster Session (even numbers) with drinks and snacksHelix B
20:50Bus to ISG HotelATC entrance
Day 3 – Tuesday, 13 June 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:05Overview of the dayCourtyard Room A & B
09:05 – 10:35Lecture: Introduction to label-free quantification by DIA/SWATH
Christina Ludwig – Technical University Munich, Germany
Courtyard Room A & B
10:35 – 11:05Coffee BreakCourtyard Room A & B
11:05 – 12:35Practical session 2: Label-free protein quantification by DIA/SWATH
Miriam Abele – Technical University Munich, Germany
Jeroen Krijgsveld – German Cancer Research Center (DKFZ)/University of Heidelberg, Germany
Christina Ludwig – Technical University Munich, Germany
Julia Mergner – Technical University Munich, Germany
Mikhail Savitski – EMBL Heidelberg, Germany
Computer Training Lab
12:35 – 13:35LunchEMBL Canteen
13:35 – 15:35Practical session 2 (cont.): Label-free protein quantification by DIA/SWATH
Miriam Abele – Technical University Munich, Germany
Jeroen Krijgsveld – German Cancer Research Center (DKFZ)/University of Heidelberg, Germany
Christina Ludwig – Technical University Munich, Germany
Julia Mergner – Technical University Munich, Germany
Mikhail Savitski – EMBL Heidelberg, Germany
Computer Training Lab
15:35 – 16:05Coffee BreakCourtyard Room A & B
16:05 – 17:05Application talk 2: Spatial and sub-cellular proteomics
Kathryn Lilley – University of Cambridge, UK
Courtyard Room A & B
17:05 – 18:05Application talk 3: Versatility of SILAC labeling to understand proteome dynamics
Jeroen Krijgsveld – German Cancer Research Center (DKFZ)/University of Heidelberg, Germany
Courtyard Room A & B
18:05 – 19:00DinnerEMBL Canteen
19:00Bus to ISG HotelATC entrance
Day 4 – Wednesday, 14 June 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:05Overview of the dayCourtyard Room A & B
09:05 – 10:05Lecture: Introduction of MSFragger for analysis of TMT data
Alexey Nesvizhskii – University of Michigan, USA
Courtyard Room A & B
10:05 – 12:05Practical session 3: Analysis of TMT and PTM data with MSFragger
Alexey Nesvizhskii – University of Michigan, USA
Daniel Polasky – University of Michigan, USA
Christina Ludwig – Technical University Munich, Germany
Mikhail Savitski – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Computer Training Lab
12:05 – 13:05LunchEMBL Canteen
13:05 – 14:35Practical session 3 (cont.): Analysis of TMT and PTM data with MSFragger
Alexey Nesvizhskii – University of Michigan, USA
Daniel Polasky – University of Michigan, USA
Christina Ludwig – Technical University Munich, Germany
Mikhail Savitski – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Computer Training Lab
14:35 – 15:05Coffee BreakCourtyard Room A & B
15:05 – 16:05Open discussion: Agenda to be set by course participantsCourtyard Room A & B
16:05 – 17:05Application talk 4: Stability proteomics
Mikhail Savitski – EMBL Heidelberg, Germany
Courtyard Room A & B
17:05 – 18:05Meet the speaker session with drinks and snacksCourtyard Room A & B
18:05Free evening
Bus downtown via ISG Hotel
EMBL bus stop
Day 5 – Thursday, 15 June 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:05Overview of the dayCourtyard Room A & B
09:05 – 10:35Lecture: Introduction to statistical analysis of proteomics data
Olga Vitek – Northeastern University, USA
Courtyard Room A & B
10:35 – 11:05Coffee BreakCourtyard Room A & B
11:05 – 12:35Practical session 4: Statistical analysis of proteomics data using MSStats
Olga Vitek – Northeastern University, USA
Miriam Abele – Technical University Munich, Germany
Devon Kohler – Northeastern University, USA
Christina Ludwig, Technical University Munich, Germany
Julia Mergner – Technical University Munich, Germany
Computer Training Lab
12:35 – 13:35LunchEMBL Canteen
13:35 – 15:35Practical session 4 (cont.): Statistical analysis of proteomics data using MSStats
Olga Vitek – Northeastern University, USA
Miriam Abele – Technical University Munich, Germany
Devon Kohler – Northeastern University, USA
Christina Ludwig, Technical University Munich, Germany
Julia Mergner – Technical University Munich, Germany
Computer Training Lab
15:35 – 16:05Coffee breakCourtyard Room A & B
16:05 – 17:05Application talk 5: Allosteric proteomics
Ilaria Piazza – MDC Berlin, Germany
Courtyard Room A & B
17:05 – 17:45Bus downtown via ISGEMBL bus stop
17:45 – 19:15Guided city tour
19:30 – 21:30Course dinner
Day 6 – Friday, 16 June 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:05Overview of the dayCourtyard Room A & B
09:05 – 10:05Application talk 6: Structural interactomics
Fan Liu – Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Germany
Courtyard Room A & B
10:05 – 12:35Breakout sessions – Discussion in groupsCourtyard Room A & B,
Flex Lab A & B
12:35 – 13:35LunchEMBL Canteen
13:35 – 15:35Presentations from breakout session & Panel discussionCourtyard Room A & B
15:35 – 16:05Recap and FarewellCourtyard Room A & B
16:05Bus to train station via ISGATC entrance

Practical Information

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, COVID-19 safety measures, meals and coffee breaks. This EMBO course includes accommodation and transportation to and from the ISG Hotel to the venue.

Academia€500
PhD Student€500
Industry€1000

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

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 you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively, you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

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

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

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

This grant covers costs related to your attendance at 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

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding 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 the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles

Hotel

Accommodation has been pre-booked for you at the ISG Hotel for the default dates of 11 to 16 June 2023 (5 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfasts, for your stay at the ISG. In case you would like to have a single room, please let us know and please note that you will be required to pay an additional cost of 31€ per night. This should be paid by you directly to the ISG during your stay. Any additional nights need to be booked and paid for by you. We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Technical requirements and event software

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Additional information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Sponsors

Event supporter:

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 events, 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.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 11 - 16 Jun 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:

  • Jeroen Krijgsveld
    German Cancer Research Center, Germany

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