Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Date: 6 - 9 May 2025, register here

Location: LUMC

Organizers: Yuri van der Burgt and Magnus Palmblad 

Fourier transform ion cyclotron resonance (FTICR) mass spectrometry  is an advanced analytical technique capable of determining molecular masses with exceptional precision and resolving power. While replaced by Orbitrap and time-of-flight mass spectrometry for many applications, it remains the method of choice for the highest mass measurement precision and analytical versatility. At the LUMC, we continue to use high-field FTICR mass spectrometry in a range of proteomics, glycomics and metabolomics applications in which this technology still outclasses other types of mass spectrometry. More recently, it has been noted that FTICR is particularly well suited for generating high-quality training data for artificial intelligence (AI) applications in mass spectrometry.
This short course will cover the basic physical principles, the data processing (which has many commonalities with Orbitrap mass spectrometry, also being a Fourier transform mass spectrometry method) and a hands-on demonstration of the 15 T FTICR at the LUMC equipped both with electrospray and MALDI ion sources.

Schedule:
May 6 - 09:00-16:00 V-03-012 Introduction to ICR and FTMS
May 7 - 09:00-16:00 T-00-008 Applications of FTICR, FTMS data processing
May 8 - 09:00-16:00 P-00-010 Lab demonstrations/theoretical exercises in groups
May 9 - 09:00-12:00 T-00-008 Discussion of exercises, summary

There is a maximum of 16 participants, registration applies on a first-come, first-served basis.

The course is free of charge for all personnel of MGC associated institutes, see cancellation and no-show rules below.

Please note that people with pacemakers cannot attend the practical part of the course, as they are not allowed to enter the laboratory! 

Practical Linux

Date:  11 February 2025 and 13 May 2025, register here
Time: 10:00 - 14:00?
Location: LUMC, room J-01-082 (route 555)

Registration applies on a first-come, first-served basis. If fully booked your name will be put on a reserve list which gives you priority for next edition.

Organizer: Mihai Lefter

After completing this short, half day, course attendees will be able to swiftly start using Linux both on a server as well as on their personal computer.
There are no prerequisites, but the Linux course is mandatory for the courses: Shark, Code management with Git, Scripting for life science researcher, and Python programming.

More information
The course is free of charge. See cancellation rules at the bottom of this page.

Code management with Git

Date: 19 February 2025 and 20 May 2025, register here

Location: LUMC, room J-01-082 (route 555)

Registration applies on a first-come, first-served basis. If fully booked your name will be put on a reserve list which gives you priority for next edition.

Organizer: Mihai Lefter

This course aims at everyone who works in the Bioinformatics field. We cover a version control system named Git. This system is widely used by software developers but can also be used for project management. By keeping track of all versions, history, etc. collaboration with colleagues is easy and your analysis will be reproducible. Knowledge of Linux is required to follow this course.

More information

The course is free of charge. See cancellation rules at the bottom of this page.

Python Programming

Date: 7 - 10 July 2025, register here

Location: LUMC, J-01-083 and Lecture room 7 (Building 1)

Registration applies on a first-come, first-served basis. If fully booked your name will be put on a reserve list which gives you priority for next edition.

Organizer: Mihai Lefter 

The course is targeted at PhD students, postdocs, or anyone willing to learn how to program in Python. Participants are assumed to have some experience with programming, but not necessarily in Python, and the UNIX shell. For this reason it is mandatory to follow the Practical Linux and Code management with git courses before.

There will be a focus on bioinformatics and programming to support scientific research in general. The program consists of four mornings with lessons and some assignments to be done in your own time (i.e., during the afternoons).

The course is free of charge for all personnel from MGC  and Erasmus MC institutes. Participants from outside these institutes pay €400. There is a maximum of 20 places. See cancellation rules at the bottom of this page. 

Scripting for Life Science Researchers

No date yet, add your name to the waiting list here; once sufficient interested people apply, a session for this course will be arranged.

Organizer: Mihai Lefter

This course is designed for researchers, who frequently handle large datasets or large numbers of files (images, sequence reads, mass spectra etc.) and who need a more efficient way of working with such data. The goal of the course is to empower students and researchers with backgrounds in biology or biomedicine to navigate, manage and perform operations on files and data and metadata in tabular text formats. The data may be microscopy images, FASTA sequences, gene ontology files, chromatograms, mass spectra or tables with data on genes or proteins. The course is not a general introduction to programming and will not deal with XML data, Web services or more advanced topics. For the Scripting course it is required to have followed the Linux course first. In case you haven’t done this yet, you can subscribe via the MGC website for next edition of the Practical Linux course.

 MGC courses: general cancellation rules for MGC members 

The courses are free of charge but please note that we have set up strict cancellation rules:

•            Free cancellation up to 1 week before the start of a one day course and up to 2 weeks before other courses

•            Cancellations after the mentioned time interval until one day before the start of the course: €50 per course day unless you have a replacement. In that case name and email address plus confirmation from the replacement is included in the cancellation email to the MGC secretariat nivard@lumc.nl 

•            In case of no-show up: €75 per course day

In collaboration with the Erasmus MC graduate school - see course program

Safely working in the Laboratory

This course is not offered face to face. You can request login details from the video recordings of the 2020 course at nivard@lumc.nl