16/12/2021 - News

Proteins form functional networks, and so do people – the first PROTrEIN summer school

by Marc Pauper and Mostafa Kalhor

Applying and going through the selection for a PhD position in PROTrEIN was challenging enough, but it did not compare to the subsequent excruciating wait for a response. However, the latter arrived approximately one week later and the wait had been well-worth it. It is impossible to forget the moment the notification arrived on the smartphone and the seconds-that-seem-like-years that it took to open the email. We had been selected to be ESRs of PROTrEIN and a major new chapter of our lives was set in motion.Several months later, it was finally time for the first official event of PROTrEIN, where all members of the network were going to gather in one (virtual) place. The first PROTrEIN Summer School was officially launched on September 10th, 2021, and while it was unfortunate that the exciting city of Barcelona could not be the venue for this event, everyone was nonetheless excited to finally have the opportunity to meet the rest of the members. The Summer School was split into three parts: the consortium meeting, the advanced proteomics course and the module on open and responsible research.

After having everyone connected in the Zoom session, Jonas Krebs and Eduard Sabidó launched the day with some introductory slides on the project’s organization, funding and timelines. It was an ideal recap of things that we had already looked up in the previous months (we were impatient, ok?), but also some helpful new information was thrown in, such as a proposed schedule for regular ESR meetings etc. The rest of the day was filled with activities to break the ice between all members and get them to interact in a fun setting. It can be difficult to achieve these goals in a videoconference setting, but we should congratulate all the people that were involved in organizing the event, such as Anna, Imma and Damjana from the CRG Training Unit. They had done an amazing job, not only with all the events and activities that were planned (and that we will go over below), but also for the simpler details such as the music playing in Zoom during the coffee breaks.

A world-wide connection

One of the first ice-breakers we did, was to open up a virtual world map and place a pin on our current location. From Tamper, Finland to Mangalore, India and from Jeonju, South Korea to Rockville, USA, there were pins scattered all around. It is an impressive feat of scientific project such as PROTrEIN, to create such diverse networks of individuals across all these time zones. And soon enough, we would all be on the European continent doing exciting research!

Express your feelings

A couple of weeks before the event, we had been asked to find and post a GIF image each to describe their feelings about ourrespective PhD projects. The old proverb says “one picture is worth a thousand words”, so you would think that an animated one would be adequate to describe these feelings. Well, wrong! There were so many feelings and thoughts in our minds regarding our forthcoming PhD project, and some of them do not even have a word dictionary. Nonetheless, we all tried our best to focus on one of those feelings and we ended up with a highly expressive wall of GIF images.


Writing this post several weeks after the events, we still vividly remember the reaction of Eduard at the end of this particular section: “Wow! This was… intense!”. It was the most suitable reaction to what was otherwise an incredibly fun activity. Thanks to Zoom’s functionality, pairs were formed and placed in separate breakout rooms with precisely two minutes to quickly get to know each other, before being abruptly interrupted and thrown into another breakout room with someone new. Do you remember the beginning of this post where we described how can a few seconds feel so long when you open an important email? Well, these 2 minutes in a breakout room with someone you barely know felt like the complete opposite! It provided mixed feelings of excitement to discover who your new partner was, while at the same time carrying over the frustration from being interrupted mid-sentence with the previous. Now we look forward to the next event (1st Winter School in Zurich) and hope that we are able to meet in person and complete all these unfinished conversations.

Advanced Proteomics course

After getting familiar with all ESRs and supervisors, it was time to focus on the concept of proteomics. We took the online advanced proteomics course from the 13th to the 17th of September, and each day consisted of two main parts. In the first part (morning), a series of lectures were provided by our supervisors and other invited professors. These lectures were provided in-depth information on various topics such as data-dependent and –independent acquisition, manual spectra annotation and even reconstruction of ancient protein sequences. We gained a lot of insight into some core, but also advanced, concepts of proteomics. One of the most interesting sessions was about the applications of machine learning to proteomics data. In the next part (afternoon), we experienced some hands-on workshops where ESRs were separated into groups to work together on a particular problem. This experience was really challenging and also exciting, mainly because we had to network with other ESRs, coming from different backgrounds, to resolve an issue at a specific time.  

Open & Responsible research

The last three days of the Summer School were dedicated to the topic of open and responsible research. The topic itself is broad enough, and through some excellent seminars/workshops we had the chance approach the matter from a variety of angles. Going into details would make what is an already pretty long post interminable, but we had the chance to learn about concepts such as data openness (and particularly the FAIR principles), result reproducibility and the various options and procedures that go into authoring and publishing scientific articles. Best of all was the opportunity we had to openly question and discuss these important matters among ourselves.We hope these are topics that we will have the chance to revisit in future posts of this blog!

We hope these are topics that will be revisited in future posts of this blog!

Latest posts

Exploring Cellular Complexity: Unveiling Single-Cell Proteomics

08/09/2023 - Journal Club

Exploring Cellular Complexity: Unveiling Single-Cell Proteomics

Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

23/08/2023 - Journal Club

Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

Peptide De Novo Sequencing  What are the ingredients of that delicious pizza?

08/08/2023 - Journal Club

Peptide De Novo Sequencing What are the ingredients of that delicious pizza?