Miriam Abele
Technical University Munich
Germany
EMBO Practical Course
Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.
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.
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.
Technical University Munich
Germany
Ghent University
Belgium
German Cancer Research Center
Germany
Northeastern University
USA
German Cancer Research Center and Heidelberg University
Germany
Karolinska Institute
Sweden
University of Cambridge
UK
Leibniz-Forschungsinstitut für Molekulare Pharmakologie
Germany
Technical University Munich
Germany
Ghent University
Belgium
Technical University Munich
Germany
University of Oxford
UK
University of Michigan Medical School
USA
Max Delbrück Center
Germany
University of Michigan Medical School
USA
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
German Cancer Research Center and Heidelberg University
Germany
Technical University Munich
Germany
EMBL Heidelberg
Germany
Course and Conference Officer
EMBL Heidelberg
Germany
Training Lab Technician
EMBL Heidelberg
Germany
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Time (Europe/Berlin) | Session | Location |
---|---|---|
13:00 | Bus to EMBL ATC | ISG Hotel |
13:30 – 14:00 | Registration, welcome and housenotes | Courtyard Room A & B |
14:00 – 14:45 | Introduction: 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 – 16:00 | Lecture: Peptide chromatography in proteomics (remote lecture) Shabaz Mohammed – University of Oxford, UK | Courtyard Room A & B |
16:00 – 16:30 | Coffee Break | Courtyard Room A & B |
16:30 – 17:30 | Flash talks 1 (odd numbers) | Courtyard Room A & B |
17:30 – 19:00 | Poster Session (odd numbers) with drinks and snacks | Helix B |
19:00 – 20:00 | Dinner | EMBL Canteen |
20:00 | Bus to ISG Hotel | ATC entrance |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 | Bus to EMBL ATC | ISG Hotel |
09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
09:05 – 10:05 | Lecture: MS technologies Dominic Helm – German Cancer Research Center (DKFZ), Germany | Courtyard Room A & B |
10:05 – 11:20 | Lecture: Peptide and protein identification Lennart Martens – Ghent University, Belgium | Courtyard Room A & B |
11:20 – 11:35 | Coffee Break | Courtyard Room A & B |
11:35 – 12:35 | Practical 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 – 13:35 | Lunch | EMBL Canteen |
13:35 – 15:05 | Practical 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 – 16:20 | Coffee break and Lab tour | Courtyard Room A & B / Proteomics Core Facility |
16:20 – 17:20 | Flash talks 2 (even numbers) | Courtyard Room A & B |
17:20 – 18:20 | Application talk 1: Cancer proteogenomics Janne Lehtiö – Karolinska Institute, Sweden | Courtyard Room A & B |
18:20 – 19:20 | Dinner | EMBL Canteen |
19:20 – 20:50 | Poster Session (even numbers) with drinks and snacks | Helix B |
20:50 | Bus to ISG Hotel | ATC entrance |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 | Bus to EMBL ATC | ISG Hotel |
09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
09:05 – 10:35 | Lecture: Introduction to label-free quantification by DIA/SWATH Christina Ludwig – Technical University Munich, Germany | Courtyard Room A & B |
10:35 – 11:05 | Coffee Break | Courtyard Room A & B |
11:05 – 12:35 | Practical 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 – 13:35 | Lunch | EMBL Canteen |
13:35 – 15:35 | Practical 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 – 16:05 | Coffee Break | Courtyard Room A & B |
16:05 – 17:05 | Application talk 2: Spatial and sub-cellular proteomics Kathryn Lilley – University of Cambridge, UK | Courtyard Room A & B |
17:05 – 18:05 | Application 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 – 19:00 | Dinner | EMBL Canteen |
19:00 | Bus to ISG Hotel | ATC entrance |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 | Bus to EMBL ATC | ISG Hotel |
09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
09:05 – 10:05 | Lecture: Introduction of MSFragger for analysis of TMT data Alexey Nesvizhskii – University of Michigan, USA | Courtyard Room A & B |
10:05 – 12:05 | Practical 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 – 13:05 | Lunch | EMBL Canteen |
13:05 – 14:35 | Practical 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 – 15:05 | Coffee Break | Courtyard Room A & B |
15:05 – 16:05 | Open discussion: Agenda to be set by course participants | Courtyard Room A & B |
16:05 – 17:05 | Application talk 4: Stability proteomics Mikhail Savitski – EMBL Heidelberg, Germany | Courtyard Room A & B |
17:05 – 18:05 | Meet the speaker session with drinks and snacks | Courtyard Room A & B |
18:05 | Free evening Bus downtown via ISG Hotel | EMBL bus stop |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 | Bus to EMBL ATC | ISG Hotel |
09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
09:05 – 10:35 | Lecture: Introduction to statistical analysis of proteomics data Olga Vitek – Northeastern University, USA | Courtyard Room A & B |
10:35 – 11:05 | Coffee Break | Courtyard Room A & B |
11:05 – 12:35 | Practical 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 – 13:35 | Lunch | EMBL Canteen |
13:35 – 15:35 | Practical 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 – 16:05 | Coffee break | Courtyard Room A & B |
16:05 – 17:05 | Application talk 5: Allosteric proteomics Ilaria Piazza – MDC Berlin, Germany | Courtyard Room A & B |
17:05 – 17:45 | Bus downtown via ISG | EMBL bus stop |
17:45 – 19:15 | Guided city tour | |
19:30 – 21:30 | Course dinner |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 | Bus to EMBL ATC | ISG Hotel |
09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
09:05 – 10:05 | Application talk 6: Structural interactomics Fan Liu – Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Germany | Courtyard Room A & B |
10:05 – 12:35 | Breakout sessions – Discussion in groups | Courtyard Room A & B, Flex Lab A & B |
12:35 – 13:35 | Lunch | EMBL Canteen |
13:35 – 15:35 | Presentations from breakout session & Panel discussion | Courtyard Room A & B |
15:35 – 16:05 | Recap and Farewell | Courtyard Room A & B |
16:05 | Bus to train station via ISG | ATC entrance |
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 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.
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.
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
Please note:
For detailed instructions, please watch our video on how to submit a course motivation letter.
For further information about registration and motivation letter submission please refer to the FAQ page.
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.
The fee waiver will cover the registration sum that you have paid to attend the course.
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.
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.
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
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.
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.
Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.
See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.
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.
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.
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.
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.
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 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.
Event supporter:
Sponsorship opportunities
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Please also note that:
Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.
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Date: 11 - 16 Jun 2023
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Application: Closed
Organisers:
Contact: Aline Schnieder