Quantitative proteomics: strategies and tools to probe biology

Time (Europe/Berlin)	Session	Location
13:45 – 14:00	Arrival and registration	ISG Hotel
14:00 – 14:15	Welcome and housenotes	Courtyard Room A & B
14:15 – 15:00	Introduction: Quantitative proteomics for biology Jeroen Krijgsveld – German Cancer Research Center (DKFZ), Germany Christina Ludwig – Technical University Munich, Germany Mikhail Savitski – EMBL Heidelberg, Germany	Courtyard Room A & B
15:00 – 16:00	Flash talks 1 (odd numbers)	Courtyard Room A & B
16:00 – 16:30	Coffee break	Courtyard Room A & B
16:30 – 18:30	Poster session with drinks and snacks (odd numbers)	Helix B
18:30 – 19:30	Dinner	EMBL Canteen

Time (Europe/Berlin)	Session	Location
08:55 – 09:00	Overview of the day	Courtyard Room A & B
09:00 – 10:00	Basic lecture: Introduction to LC-MS/MS and sample preparation in proteomics Mandy Rettel – EMBL Heidelberg, Germany	Courtyard Room A & B
10:00 – 10:30	Coffee break	Courtyard Room A & B
10:30 – 11:15	Basic lecture: Introduction to MS-based protein quantification Christina Ludwig – Technical University Munich, Germany	Courtyard Room A & B
11:15 – 12:00	Lecture: Peptide and protein identification Lennart Martens -VIB-UGent Center for Medical Biotechnology, Ghent University, Belgium	Courtyard Room A & B
12:00 – 13:00	Lunch	EMBL Canteen
13:00 – 15:00	Practical session 1: Peptide and protein identification Lennart Martens – VIB-UGent, Belgium	Computer Training Lab
15:00 – 15:30	Coffee break	Courtyard Room A & B
15:30 – 16:30	Practical session 1: Peptide and protein identification Lennart Martens – VIB-UGent, Belgium	Computer Training Lab
16:30 – 17:30	Flash talks 2 (even numbers)	Courtyard Room A & B
17:30 – 18:30	Pizza dinner	Helix B
18:30 – 20:30	Poster Session with drinks and snacks (even numbers)	Helix B

Time (Europe/Berlin)	Session	Location
08:55 – 09:00	Overview of the day
09:00 – 10:00	Lecture: Introduction to FragPipe computational proteomics platform Alexey Nesvizhskii – University of Michigan, USA	Courtyard Room A & B
10:00 – 10:30	Coffee break	Computer Training Lab
10:30 – 12:00	Practical session 2: Analysis of quantitative proteomics data and PTM data with MSFragger and FragPipe Alexey Nesvizhskii – University of Michigan, USA	Computer Training Lab
12:00 – 13:00	Lunch	EMBL Canteen
13:00 – 14:30	Practical session 2: Analysis of quantitative proteomics data and PTM data with MSFragger and FragPipe Alexey Nesvizhskii – University of Michigan, USA	Computer Training Lab
14:30 – 15:00	Coffee break	Courtyard Room A & B
15:00 – 16:00	Good Scientific Practice in the Era of Large Language Models	Courtyard Room A & B
16:00 – 17:00	Treasure hunt	ATC
17:00 – 18:00	Application talk 1: Protein regulation in immuno-oncology Kelly Stecker – Utrecht University, The Netherlands	Courtyard Room A & B
18:00	Free evening

Time (Europe/Berlin)	Session	Location
08:55 – 09:00	Overview of the day	Courtyard Room A & B
09:00 – 10:30	Lecture: Introduction to DIA Vadim Demichev – Aptila Biotech, Germany	Computer Training Lab
10:30 – 11:00	Coffee break	Computer Training Lab
11:00 – 12:30	Practical session 3: Global proteome analysis with DIA-NN Vadim Demichev – Aptila Biotech, Germany Jeroen Krijgsveld – German Cancer Research Center (DKFZ), Germany Christina Ludwig – Technical University Munich, Germany Julia Mergner – Technical University Munich, Germany Mikhail Savitski – EMBL Heidelberg, Germany	Computer Training Lab
12:30 – 13:30	Lunch	EMBL Canteen
13:30 – 15:30	Practical session 3: Global proteome analysis with DIA-NN Vadim Demichev – Aptila Biotech, Germany Jeroen Krijgsveld – German Cancer Research Center (DKFZ), Germany Christina Ludwig – Technical University Munich, Germany Julia Mergner – Technical University Munich, Germany Mikhail Savitski – EMBL Heidelberg, Germany	Computer Training Lab
15:30 – 16:00	Coffee break	Computer Training Lab
16:00 – 17:00	Application talk 2: Dynamic regulation of protein post-translational modifications Ana Martinez – CNIC – Spanish National Center for Cardiovascular Research, Spain	Courtyard Room A & B
17:00 – 18:00	Open panel discussion (agenda to be set by course participants)	Courtyard Room A & B
18:00 – 19:00	Career dinner with Meet the speakers	EMBL Canteen

Time (Europe/Berlin)	Session	Location
08:55 – 09:00	Overview of the day	Courtyard Room A & B
09:00 – 10:30	Lecture: Introduction to statistical analysis of proteomics data Sarah Szvetecz – Northeastern University, USA	Courtyard Room A & B
10:30 – 11:00	Coffee break	Courtyard Room A & B
11:00 – 12:30	Practical session 4: Statistical analysis of proteomics data using MSStats Devon Kohler – Northeastern University, USA Sarah Szvetecz – Northeastern University, USA	Computer Training Lab
12:30 – 13:30	Lunch	EMBL Canteen
13:30 – 15:30	Practical session 4: Statistical analysis of proteomics data using MSStats Devon Kohler – Northeastern University, USA Sarah Szvetecz – Northeastern University, USA	Computer Training Lab
15:30 – 16:00	Coffee break	Courtyard Room A & B
16:00 – 17:00	Application talk 3: Single-cell proteomics Jeroen Krijgsveld – German Cancer Research Center (DKFZ), Germany	Courtyard Room A & B
17:00 – 17:45	Bus downtown via ISG	ATC Entrance
17:45 – 19:15	Guided city tour	Downtown Heidelberg
19:15 – 22:00	Course dinner downtown	Downtown Heidelberg

Time (Europe/Berlin)	Session	Location
08:55 – 09:00	Overview of the day	Courtyard Room A & B
09:00 – 10:00	Application talk 4: Functional proteomics Mikhail Savitski – EMBL Heidelberg, Germany	Computer Training Lab
10:00 – 10:30	Coffee break and Proteomics Core Facility tour	Courtyard Room A & B
10:30 – 12:30	Group Challenge – Proteomics research topic Julia Mergner	Courtyard Room A & B
12:30 – 13:30	Lunch	EMBL Canteen
13:30 – 15:00	Presentations from Group Challenge	Courtyard Room A & B
15:00 – 15:30	Treasure hunt results	Courtyard Room A & B
15:30 – 15:45	Course debrief and feedback with participants	Courtyard Room A & B

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

Your registration for the event includes:

• Admission to the event
• Possibility to submit an abstract (if applicable)
• Meals and coffee breaks
• Course materials
• Access to the e-learning platform
• A letter to support your visa application (for more information, check the ‘Travel and accommodation’ tab)

For this EMBO course, the fees include accommodation and transportation to and from the ISG Hotel to the venue

Academia	€500
PhD Student	€500
Industry	€1000

Confirmation and payment

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

Cancellation policy

If you are no longer able to take part in the course, please inform your course contact responsible for this event. Your registration and the submitted motivation letter will be deleted.

Please also check our Terms and Conditions for the cancellation policy.

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 2,000 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.

Please note it is not possible to apply after the motivation letter deadline!

Selection

The selection results will be announced by email to all applicants. We aim to announce 3 weeks (21 days) after the motivation letter submission deadline but delays may occur.

Further details

For further information about

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of travel grants, childcare grants, and accessibility grants.

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

Travel grant

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

• 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.

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. Receipts must be provided via email with your signature for all costs incurred within two months of completion of travel.

Childcare grants

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers, and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter, child-care facility, or travel costs for a caregiver. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

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

European Foundation for Urology (EFU) Grants

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

The EFU fellowship covers full costs related to your attendance at the course (registration fee, travel and accommodation costs). The grant is restricted to supporting academic or clinical PhD students and postdoctoral researchers whose primary research areas maybe on cancers broadly, but must especially demonstrate in the course motivation letter clear relatability or knowledge transferability to urological cancers (prostate, bladder, kidney, testicular, penile, and urethral cancers).

To qualify for the EFU fellowship, applicants are required to include a brief statement in their motivation letter explaining how this is evident.

The scope of the full grant includes the following:

• Fee waver will cover the registration sum that you have paid to attend the course

• additionally up to €400 for participants travelling to an EMBL Course within Europe or

• additionally up to €1000 for participants travelling to an EMBL Course from outside Europe

The funded participants are required to submit a personal curriculum vitae, as well as a letter of recommendation from their host institution or laboratory. In addition, awardees must provide a short report within 30 days after the course completion, describing how their participation benefited them and contributed to the advancement of their research (up to 2,000 characters).

EMBO accessibility grant

For EMBO Practical Course participants with accessibility needs, there is the possibility to apply for an accessibility grant to offset costs incurred by participants or speakers when participating at a course. Eligible costs include costs incurred for equipment or adaptations to the course environment, or travel costs for an event companion to assist the participant or speaker during the course where necessary. While we do our best to accommodate needs, please note that extensive changes to the course environment might not be possible. Priority will be given to early-stage researchers.

A maximum amount of €500 can be awarded per participant applying for an EMBO accessibility grant. In order to apply for this grant for EMBO Practical Courses, you must be registered by the application deadline. 

Application

You may apply for financial assistance when submitting your motivation letter. In the application system, you will be asked which type of grant you want to apply for.

Applications for financial support will not influence the outcome of the selection results.

Results

Grant allocations are announced by email to all applicants after the selection results.

Selection for financial assistance 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.

Please note that for childcare grants, priority will be given to early-stage researchers.

Further details

Check out this list of external funding opportunities. 

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

Visa

We can send you a registration confirmation to support your visa procedure (not an official invitation letter). Please contact the Conference Officer responsible for your event. Read our FAQ for more information.

Travel

If you are travelling to Heidelberg via aeroplane, train, car, or long-distance bus, you can find useful information on our travel information page.

Accommodation

Accommodation in twin rooms, including breakfast is also part of the registration fee. Accommodation will be booked for the selected participants at the ISG Hotel for the default dates of 7 to 12 March 2026 ( 5 nights).

In case you would like to have a single room, please let the hotel know and please note that you will be required to pay a surcharge per night (availability of single rooms may be limited). This should be paid by you directly to the ISG Hotel during your stay.

We recommend that all course participants stay at the ISG Hotel for the course.

Local transportation

Course shuttle buses

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.

Other local transportation

In addition to the shuttle busses, there is also the public bus 28 that serves the EMBL campus and taxis can be easily booked at any time. For more information, please refer to the local transportation (RNV) website.

You may also walk from the ISG Hotel to EMBL (takes up to 30 minutes)

Map to walk from ISG Hotel to EMBL

Further details

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

For more information about accommodation and travel, please refer to the FAQ page.

Here you will find useful information for when you are onsite at the event.

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the computer training lab or wet labs.

Internet

Wi-Fi is available on campus using the EMBL-Events network and the event specific password, which will be provided on site. The eduroam network (secure, worldwide roaming access service developed for the international research and education community) is also available.

Photography

During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Charging stations

There are lockers available next to the stairs leading down into the Auditorium. You will find some of those equipped with sockets to charge your smartphone/tablet etc.

In most places the electricity is 220 volts AC (50 cycles). An adaptor and a plug that fits the German socket may be needed for your appliances/laptop (i.e. American, Japanese, etc.). A USB charging station for electronic devices is available at the registration desk.

Printing

We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Luggage

There are lockers available on-site to store your luggage, which require a 2 EURO coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the course.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the course.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Room for prayers, meditation, and yoga

There is a room for prayer, yoga, and meditation, located on level E0 behind the Auditorium. Please be respectful of others using the room.

EMBL campus map

Health and safety notes

Please take a moment to read our health and safety policy.

• Do not smoke in any EMBL building.
• Eating and drinking is prohibited in the Auditorium and all laboratories.
• Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required

• The first aid room is located next to the ATC Registration Desk (room 10- 205).
• Dial the Emergency number 222 from any EMBL internal phone only.
• Be prepared to answer the following questions: Where is the accident? What happened? How many injured?
• Emergency number 06221-387 7821 from mobile phones.
• Please report all accidents to the conference officer at the registration desk.

In case of fire

• Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
• A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
• Do not use the lifts.

Beyond first aid

The Heidelberg University Hospital or ‘Universitätsklinikum‘ has a 24 hour accident and emergency facility and is at ‘Im Neuenheimer Feld 672’. It is a 8km or a 20 minute taxi ride away from EMBL. In a medical emergency, the ambulance service generally transports patients to this hospital.

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg.

The EMBL course and conference office team are able to advise you on where to turn for emergency or non-emergency medical treatment in Heidelberg and can assist you in making appointments and / or arranging transport to get to the pharmacy or a doctor of your choice if necessary. Please note, we are not however permitted to personally accompany you off-campus.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

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 and terms and conditions on our Information for Participants page.