Hands-on course for sample preparation and data analysis in proteomics

Time (Europe/Berlin)	Speaker	Location
08:30 – 09:00	Bus from hotel to EMBL ATC Entrance	Premier Inn Hotel
09:00 – 09:15	Registration and welcome	Flex Lab A & B
09:15 – 09:30	Course overview and introduction to Proteomics Core Facility	Flex Lab A & B
09:50 – 10:30	Flash talks by participants	Flex Lab A & B
10:30 – 10:45	Coffee Break	Courtyard Room A & B
10:45 – 12:00	Lecture: Sample preparation Mandy Rettel – EMBL Heidelberg, Germany	Flex Lab A & B
12:00 – 13:00	Lunch	EMBL Canteen
13:00 – 13:15	Introduction to Practicals	Flex Lab A & B/ Training Lab B
13:15 – 15:15	Practical 1: Cell lysis, Solubility assay, Benzonase treatment, Protein determination by Tryptophan assay	Training Lab B
15:15 – 15:45	Coffee Break	Courtyard Room A & B
15:45 – 17:45	Practical 2: Reduction & alkylation, SP3 protocol & digestion, Chloroform/Methanol precipitation & digestion	Training Lab B
17:45 – 18:30	MS- Game	Flex Lab A & B/ Training Lab B
18:30 – 20:30	Dinner	EMBL Canteen

Time (Europe/Berlin)	Speaker	Location
09:00 – 09:10	Overview of the day	Flex Lab A & B/ Training Lab B
09:10 – 10:25	Practical 3: SDC precipitation and desalting Phospho sample, Peptide extraction & TMT labelling of solubility sample	Training Lab B
10:25 – 10:55	Lecture: TMT theory and technical aspects Michal Nadler-Holly – Thermo Fisher Scientific, Germany	Flex Lab A & B
10:55 – 11:10	Coffee break & Quenching at end of coffee break	Courtyard Room A & B
11:10 – 12:10	Lecture: Phosphoproteomics Jennifer Schwarz – EMBL Heidelberg, Germany	Flex Lab A & B
12:10 – 13:10	Lunch	EMBL Canteen
13:10 – 14:10	Practical 4: Multiplexing, Sample desalting, Fe-IMAC enrichment	Flex Lab A & B
14:15 – 15:40	Lecture: Introduction to MS technology Dominic Helm – MD Anderson Cancer Center, USA	Flex Lab A & B
15:40 – 16:10	Q&A session with coffee
16:10 – 16:55	Practical 5: Load samples on Mass spec & Facility tour	Proteomics Core Facility
16:55 – 17:30	Lecture: Workflow overview Frank Stein – EMBL Heidelberg, Germany	Flex Lab A & B
17:30 –	Free evening

Time (Europe/Berlin)	Speaker	Location
09:00 – 09:10	Overview of the day	Computer Training Lab
09:10 – 09:40	Lecture: Raw file analysis with Freestyle Michal Nadler Holly – Themo fisher scientific, Germany	Computer Training Lab
09:40 – 10:30	Lecture: Raw file processing with FragPipe Frank Stein – EMBL Heidelberg, Germany	Computer Training Lab
10:30 – 10:50	Coffee break	Courtyard Room A & B
10:50 – 12:00	Computer Practical: Analysis of own solubility data with FragPipe	Computer Training Lab
12:00 – 13:00	Lunch	EMBL Canteen
13:00 – 14:00	Lecture: What data can tell you about your experimental workflow? Frank Stein – EMBL Heidelberg, Germany	Computer Training Lab
14:00 – 14:25	Coffee break	Courtyard Room A & B
14:25 – 16:25	Practical: Analysis of own Phosphoproteomics data with FragPipe	Computer Training Lab
16:25 – 16:50	Coffee break	Courtyard Room A & B
16:50 – 17:50	Computer Practical: Usage of bioinformatics tools Jennifer Schwarz – EMBL Heidelberg, Germany	Computer Training Lab
17:50 – 18:05	Bus to restaurant
18:05 – 20:05	Outside Dinner
20:05 – 20:20	Bus return to hotel

Time (Europe/Berlin)	Speaker	Location
09:00 – 09:10	Overview of the day	Flex Lab A & B
09:10 – 10:25	Lecture: Quantitative and statistical data analysis workflow Frank Stein – EMBL Heidelberg, Germany	Computer Training Lab
10:25 – 10:45	Coffee break	Courtyard Room A & B
10:45 – 11:45	Computer Practical: Fragpipe Analyst solubility data	Computer Training Lab
11:45 – 12:45	Lunch	EMBL Canteen
12:45 – 13:45	Computer Practical: Fragpipe Analyst phospho data	Computer Training Lab
13:45 – 14:30	Lecture: Applications of proteomics Mikhail Savitski – EMBL Heidelberg, Germany	Flex Lab A & B
14:30 – 16:30	Q&A session: Discussion of individual projects with PCF	Flex Lab A & B
16:30 – 16:45	Final remarks and closing	Flex Lab A & B
16:45	Bus to Heidelberg train station and city center

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration fees

Your registration for this course 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)

Accommodation and travel are not included in the fees — participants are expected to book and pay their own expenses.

Academia	€615
PhD Student	€615
Industry	€1125

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.

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.

Further details

For further information about registration, please refer to the FAQ page.

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.

Further details

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

Financial assistance

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

Your place in the meeting 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 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.

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 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 or child-care facility and 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

Application

You can apply for financial assistance in the submission portal by the abstract deadline. Read the instructions on how to apply for financial assistance. Only submissions for financial assistance will be accepted. Presentation abstracts cannot be submitted here and will be declined. 

In your application you will be asked to summarise your current work,  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 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

A selection process will take place with the results announced by email to all applicants / submitters. We aim to announce 3 weeks (21 days) after the abstract submission deadline but delays may occur.

Selection results do not impact your admission to the meeting. Selection for registration fee waivers and travel grants 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.

Childcare grants will be allocated in the same timeframe (6-8 weeks before the event start date). Please note that 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 is not included in the registration fee.

A mix of single and twin rooms have been reserved for 3 nights from 16 to 19 June 2026 at the Premier Inn hotel. Single rooms are limited and will be available on a first come, first served basis.

After the selection process, selected participants should contact the hotel directly to make a booking with a booking code (code of your course, e.g. SDP26-01) by the deadline of 19 May 2026.

We recommend that all course participants stay at the dedicated hotel for the course.

Local transportation

Course shuttle buses

Shuttle buses will go from the Premier Inn 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 travel and accommodation, 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 auditorium.

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 conference.

Lost and found

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

EMBL merchandise

If you are interested in purchasing EMBL merchandise (products presented in the glass display in the registration area), please email the EMBL shop to place an order.

Kindly note the EMBL shop is only open upon request and all purchases must be made in cash (Euros only).

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.

(delete if no technical requirements for this course!)

Technical requirements

Below you will find the software and technical requirements for this course. You will need admin rights to be able to install the software on your computer and we recommend you try this before the course. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.

Add your software name here

Add a descritpion about your software here and any other important info

Additional 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. 

Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course.

Other information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

DELETE THIS TAB IF COURSE IS NOT HYBRID!!

Guidelines

• Do not broadcast the course to unregistered participants.
• Do not share your login details with others.
• You are encouraged to post on social media about the event. Post unless the speaker specifically says otherwise, but be mindful of unpublished data. 
• Please do not capture, transmit or redistribute data presented at the meeting.
• Video library of the recorded talks during the event and for 4 weeks afterwards. Please note: at the request of individual speakers, some talks are not recorded.

Additional information can be found in our Code of Conduct.

How to ask questions

Questions during and after the talks can be asked in the live streaming platform. If time runs out or you think of a question later, you can use the EMBL eCampus forum or send a direct message to the speaker/trainer.

Time zone

The programme is planned based on the Europe/Berlin time zone, unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accommodate as many time zones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.

Please find additional information including FAQs and terms and conditions on our Information for Participants page.