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Hands-on course for sample preparation and data analysis in proteomics – Course and Conference Office

EMBL Course

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

Overview

Course overview

The course will give an introduction to the theoretical aspects of the analysis of proteins/peptides by mass spectrometry. Participants will get hands-on experience in sample preparation for a quantitative comparison across samples and perform a state of the art sample preparation and tandem mass tag labelling. Samples prepared by the participants will be measured by liquid chromatography-tandem mass spectrometry. In a session focused on bioinformatics analysis, participants will use FragPipe and FragPipe-Analyst in order to process the acquired data.

Audience

The course is intended for scientists that use or want to use proteomics for their research. Applicants should have an understanding of protein biology and should know the principle of proteomics. Ideally, they have some prior experience with proteomics either directly or through collaborators or facilities.

Modules

  • Sample preparation and data acquisition
  • Introduction to MS technology
  • Useful online tools for proteomics
  • Applications in proteomics
  • TMT history, theory, and applications
  • Experimental design principles
  • From spectra to spreadsheet tables with FragPipe
  • Data assessment (quality control) from spreadsheet outputs
  • Differential abundance analysis with FragPipe Analyst

Learning outcomes

  • State of the art sample preparation
  • Learning which aspects of sample preparation can influence the outcome of the experiment
  • Getting insights into different proteomics applications
  • Optimal experimental design
  • Basic understanding of data analysis
  • Visualisation of proteomics data

Speakers

Speakers, trainers, and staff

Michal Nadler-Holly

Thermo Fisher Scientific

Germany

Scientific Organisers

Event organisers

Swetlana Krez

Scientific Training Officer

EMBL Heidelberg

Germany

Julia Patricia Nohle

Course and Conference Officer

EMBL Heidelberg

Germany

Preliminary programme

Are you on social media? Post using #EMBLProteomics and don’t forget to tag @EMBLEvents.

  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Tuesday 3 December 2024
Time
(Europe/Berlin
)
ProgrammeLocation
09:00 – 09:15Registration and welcomeFlex Lab A & B
09:15 – 09:45Introduction to EMBL and housenotes incl. Lab safetyFlex Lab A & B
09:45 – 10:15Course overview and introduction to Proteomics Core FacilityFlex Lab A & B
10:15 – 10:45Icebreaking activity: Flash talks by participants Flex Lab A & B
10:45 – 11:00Coffee BreakFlex Lab A & B
11:00 – 12:00Lecture: Sample preparation
Mandy Rettel – EMBL Heidelberg, Germany
Flex Lab A & B
12:00 – 13:00LunchEMBL Canteen
13:15 – 14:30Practical 1: Cell lysis, Solubility assay
Per Haberkant – EMBL Heidelberg, Germany
Mandy Rettel – EMBL Heidelberg, Germany
Jennifer Schwarz – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Training Lab B
14:30 – 15:15Practical 2: Protein determination by Tryptophan assay
Per Haberkant – EMBL Heidelberg, Germany
Mandy Rettel – EMBL Heidelberg, Germany
Jennifer Schwarz – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Training Lab B
15:15 – 15:45Coffee breakFlex Lab A & B
15:45 – 17:15Practical 3: Reduction & alkylation, SP3 protocol & digestion
Per Haberkant – EMBL Heidelberg, Germany
Mandy Rettel – EMBL Heidelberg, Germany
Jennifer Schwarz – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Training Lab B
17:15 – 18:15MS-gameFlex Lab A & B/ Training Lab B
18:15 – 19:45DinnerEMBL Canteen
Day 2 – Wednesday 4 December 2024
Time
(Europe/Berlin
)
ProgrammeLocation
09:00 – 09:15Overview of the dayFlex Lab A & B/ Training Lab B
09:15 – 10:10Practical 4: Peptide extraction, TMT labelling
Per Haberkant – EMBL Heidelberg, Germany
Mandy Rettel – EMBL Heidelberg, Germany
Jennifer Schwarz – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Training Lab B
10:10 – 10:20Coffee breakFlex Lab A & B
10:20 – 10:50Lecture: TMT theory and technical aspects
Michal Nadler-Holly – Thermo Fisher Scientific, Germany
Flex Lab A & B
10:50 – 11:30Lecture: TMT application
Mikhail Savitski – EMBL Heidelberg, Germany
Flex Lab A & B
11:30 – 12:30Practical 5: Quenching, Multiplexing, Sample desalting
Per Haberkant – EMBL Heidelberg, Germany
Mandy Rettel – EMBL Heidelberg, Germany
Jennifer Schwarz – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Training Lab B
12:30 – 13:30Lunch breakEMBL Canteen
13:30 – 15:00Lecture: Introduction to MS technology
Dominic Helm – German Cancer Research Center (DKFZ), Germany
Flex Lab A & B
15:00 – 15:30Q&A session with coffeeFlex Lab A & B
15:30 – 16:45Practical 6: Load samples on Mass spec, Facility tour
Per Haberkant – EMBL Heidelberg, Germany
Mandy Rettel – EMBL Heidelberg, Germany
Jennifer Schwarz – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Proteomics Core Facility
16:45 – 17:30Lecture: Workflow overview
Frank Stein – EMBL Heidelberg, Germany
Flex Lab A & B
17:45Free evening
Day 3 – Thursday 5 December 2024
Time
(Europe/Berlin
)
ProgrammeLocation
09:00 – 09:15Overview of the dayComputer Training Lab
09:15 – 10:30Lecture: Raw file processing with MS Fragger
Frank Stein – EMBL Heidelberg, Germany
Computer Training Lab
10:30 – 10:50Coffee breakComputer Training Lab
10:50 – 12:00Computer Practical: Analysis of own data with Fragpipe
Per Haberkant – EMBL Heidelberg, Germany Mandy Rettel – EMBL Heidelberg, Germany Jennifer Schwarz – EMBL Heidelberg, Germany Frank Stein – EMBL Heidelberg, Germany
Computer Training Lab
12:00 – 13:00Lunch breakEMBL Canteen
13:00 – 14:00Lecture: What data can tell you about your experimental workflow?
Frank Stein – EMBL Heidelberg, Germany
Computer Training Lab
14:00 – 14:10Coffee breakComputer Training Lab
14:10 – 15:45Lecture/Practical: Experimental design
Sarah Kaspar – EMBL Heidelberg, Germany
Computer Training Lab
15:45 – 16:00Coffee breakComputer Training Lab
16:00 – 17:00Computer Practical: Usage of bioinformatics tools
Per Haberkant – EMBL Heidelberg, Germany
Mandy Rettel – EMBL Heidelberg, Germany
Jennifer Schwarz – EMBL Heidelberg, Germany
Frank Stein – EMBL Heidelberg, Germany
Computer Training Lab
17:10 – 18:00Bus downtown
18:00 – 19:00Heidelberg Christmas market
19:00 – 21:30Dinner downtown
Day 4 – Friday 6 December 2024
Time
(Europe/Berlin
)
ProgrammeLocation
09:00 – 09:15Overview of the dayFlex Lab A & B
09:15 – 10:30Lecture: Quantitative and statistical data analysis workflow
Frank Stein – EMBL Heidelberg, Germany
Computer Training Lab
10:30 – 10:50Coffee breakComputer Training Lab
10:50 – 11:30Computer Practical: Fragpipe Analyst
Per Haberkant – EMBL Heidelberg, Germany Mandy Rettel – EMBL Heidelberg, Germany Jennifer Schwarz – EMBL Heidelberg, Germany Frank Stein – EMBL Heidelberg, Germany
Computer Training Lab
11:30 – 12:30Lecture: Applications in proteomics
Per Haberkant – EMBL Heidelberg, Germany
Flex Lab A & B
12:30 – 13:30LunchEMBL Canteen
13:30 – 14:15Lecture: Phosphoproteomics
Jennifer Schwarz – EMBL Heidelberg, Germany
Flex Lab A & B
14:15 – 15:30Q&A session: Discussion of individual projects with PCFFlex Lab A & B
15:30 – 16:00Imaging Centre tourComputer Training Lab
16:15Bus to Heidelberg train station and city center

Practical information

Registration fees and motivation letter

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

Registration fees include admission, course materials, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses.

Academia€575
PhD Student€575
Industry€1100

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 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/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

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 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 registration fee waivers and travel grants during the motivation letter or abstract 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 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.

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 travel

Hotel

Accommodation is not included in the registration fee. Participants are expected to book and pay for their own accommodation. A mix of single and twin rooms have been reserved for 4 nights, 2 – 6 December 2024, at ISG 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 booking code SDP24-01 by the deadline of Tuesday, 5 November 2024. We recommend that all course participants stay in the dedicated hotel for the course.

Travel information

For travel information, please see here.

If you are travelling to the conference within Germany then you are eligible for the Deutsche Bahn ‘Event Ticket’ (called the ‘Veranstaltungsticket’ in German). This will result in a lower ticket price if your travel distance to Heidelberg is more than 100 km. You need to provide proof of your event attendance when purchasing the ticket.

For more information in English see here or in German see here.

You can book your ticket here.

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

On-site information

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a wide 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 laboratories.

Electricity and charging station

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.

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 or get in contact with your Course Organiser.

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

Health and safety notes

Please read EMBL’s COVID-19 safety policy for on-site events.
Do not smoke in any EMBL building.
Eating and drinking is prohibited in 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.
  • 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…

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. In any case, the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary.

Internet

Wi-Fi is available on campus. Log in 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.

Lost and found

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

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.

Nursing room

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

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.

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.

Room for prayer, yoga, and meditation

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

Sightseeing

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

Travel to and from the venue

During the event, we provide conference shuttle buses to and from EMBL. In addition, there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. Information on the shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page.

Additional information

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

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

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 partner

Event 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 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: 3 - 6 Dec 2024

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: 3 Sep 2024


Organisers:


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