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1st EU-COST Seed Course on Imaging Mass Spectrometry

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Topic: Science  |  Series: My Journey to PhD
Journal of Proteomics Volume 75, Issue 16, 30 August 2012, Pages 5113–5121"COST is an intergovernmental framework for European Cooperation in Science and Technology, allowing the coordination of nationally-funded research on a European level." "COST enables break-through scientific developments leading to new concepts and products and thereby contributes to strengthen Europe’s research and innovation capacities." These are words form the official website www.cost.eu.

COST is, by telling it with my own words, an organization, which brings scientists from all over the Europe together. It supports co-operations, strengthens relationships, improves communication, helps research sharing and also supports students education.

There are nine different areas involved within COST activities. One of the domains that currently touches me the most is the domain of Biomedicine and molecular Biosciences and its action BM1104: Mass Spectrometry Imaging: New Tools for Healthcare Research.

One of the recent students supporting activity took place at FOM Institute AMOLF in Amsterdam. It was called 1st EU-COST Seed Course on Imaging Mass Spectrometry. During three days of lectures and practical lab training it provided basic knowledge on Mass Spectrometry Imaging (MSI). The course was held from Tuesday October 2nd to Thursday October 4th.

Because I already had the basic MSI knowledge, I could focus my attention to more delicate details during the lectures, which I wouldn't probably pay attention to couple of months earlier. Moreover I was introduced to a bunch of great people from other European labs, who came along to be a part of the course. And here is what it brought us from the scientific point of view.


On Tuesday we were at first provided with information about the basic workflow of MSI through a lecture given by Ron Heeren (AMOLF). Josephine Bunch from University of Birmingham was than talking about sample preparation for imaging.

As in any other analytical technique, a flawless optimized sample prep is crucial, as we could make sure personally during the afternoon in the labs. We were divided into 8 groups (couples) and each of the couple was about to perform a different sample preparation and subject the sample to analysis on various instruments. We all came through different steps of sample preparation: sectioning of a rat brain on a microtome, washing of the tissue sections by different approaches, enzymatic digestion, matrix of choice application and alternatively also gold coating.

Regarding the instruments we could either look at intact proteins on Ultraflex (MALDI TOF/TOF), or search for small molecules on BioTRIFT II (SIMS-TOF), or look up the tryptic peptides or lipids on Synapt (MALDI Q-TOF). We did not use the tissue for a regular imaging experiment (that would come next day), but we focused only on fast profiling

The purposes of the afternoon playing around were 1/ to see, how the sample preparation can influence what we can actually observe on the tissue, 2/ to try different sample prep steps and their approaches and 3/ to learn which types of instruments are suited the best for different classes of molecules.


On Wednesday morning we had time to go through our results obtained during previous afternoon and we prepared one PowerPoint slide to show the others, what were our observation and how the chosen sample preparation influenced our results.

I was in a group, which used SIMS for profiling of the small molecules from the tissue. Our sample preparation was quite easy, as we only sectioned the tissue and without any additional washing we only applied golden layer on top of it and analyzed it directly. What we observed, was that the gold coating was suppressing the signal of many lipids - for example signal for phosphocholine head group (m/z 184) was extremely less intense when compared to non-gold coated sample. On the other hand, the gold enhanced the signal of cholesterol (m/z 369), building also a cluster with it.

SIMS influence of gold coating

The results of all groups were presented during lunch and we chose three protocols to be employed within the following afternoon, when we would prepare three samples for over night imaging experiment.

Before we went to labs, we received another portion of theoretical knowledge from Liam McDonell (Leiden University Centrum of Medicine) who was talking about basic data analysis strategies and from Axel Walch (Helmholtz Zentrum in Munich) who provided us with a lecture regarding histopathology.

We spent the evening on a course dinner, which took place in a very atypical restaurant - Lab 111. It was an old autopsy room, which was turned into a restaurant. The food and service were excellent and I would just recommend it to visit. (Btw. I ordered fish - just in case. :-D )


Thursday morning was again a lecture time. Garry Corthals from University of Turku, Finland spent three hours on peptide and protein identification strategies and database searches.

The afternoon was spent on data analysis. As we could see, data mining is one of the MSI challenges. Imagine, you collect couple of gigabytes of data, which you have to reasonably evaluate. That is were different approaches of multivariate analysis and statistics come in handy. We were shown several programmes for data processing - DataCube Explorer, BioMap... and we also tried some basic search in proteomics databases such as Mascot.

The course was ended in the late afternoon by several drinks. We all got a CD with lectures in pdfs and a list of participant's e-mails, so we can stay in touch. Next COST course regarding MSI is about the take place in Lund, Sweden next month. Hope to see you there! :-)

More information on COST MSI actions is provided also here.

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