5 Years Quantitative Proteomics Course

 

Meet Christina Ludwig (CL), Jeroen Krijgsveld (JK) and Mikhail Savitski (MS) – organisers of the EMBO Practical Course: Quantitative Proteomics: Strategies and Tools to Probe Biology (21 – 26 June 2020). This year marks the course’s 5th anniversary and since 2016 it has grown in popularity and application numbers, reaching 164 applications for 24 seats in 2018. Christina, Jeroen and Mikhail share with us how the course has developed over the years and what their vision is for its future.

 1.  This year marks the 5th anniversary of the Quantitative Proteomics course. Back in 2016, why did you decide to organise it?

JK: The main motivation to initiate the course was because proteomics has become a mature technology that is increasingly being used by biologists to identify proteins, their modifications, interactions etc. However, few biologists have direct access to mass spectrometers, so they use them via collaborators or core facilities. They then get the results in a tabular form, often in a large excel sheet, from which they extract biological interpretation of the experiment. Importantly, we felt that the area between handing in a sample for mass spectrometric analysis and receiving the results was largely a black box. So in the course we aimed to demystify this, and explain the principles and strategies to generate information from raw MS data, and to train them in the use of computational tools to achieve this. Also, we aimed to give insight that proteomics can be done in various ways, so that participants may design their experiments such that they best address the question they are looking to answer. Finally, we aimed to equip participants with some terminology that will help them to communicate with their MS-collaborators, and ask the right questions. Because in many cases proteomics remains a team effort!

2. How has the course developed since?

JK: Proteomics is a very broad field with many mass spectrometric approaches, methods for data analysis and biological applications, making it impossible to cover this in a 1-week course. While in all editions of the course we have maintained a core that explains the main principles in proteomics and covers all of the current state-of-the-art quantitative technologies used in proteomics. Additionally, we have included other elements that varied over the years, to highlight emerging topics or specific application areas, e.g. in structural biology or immunology. This year, we are happy to include a module focusing on statistical analysis of large-scale proteomic data, which is a recurrent issue in almost any proteomics experiment.

3. How do you choose which bioinformatics tools to cover in the course?

JK: There is an increasing number of bioinformatic tools that can analyse the same data using different underlying algorithms. Several of them have matured a lot over the years, making them more robust or have additional functionality. It is not always easy for anyone to know, when looking for an ‘analysis pipeline’, which tool can be best used. It can actually be a bit confusing that the same data can produce different results depending on the tool that is used, while at the same time none will be wrong. So instead of telling which tool is the best, we explain some of the underlying assumptions and the influence one has by choosing certain settings. I think for a researcher it is more important to justify how the data were processed, instead of saying that they used a certain software tool.

4. What could the techniques in this course be used for in the bigger picture?

CL: Proteomics technologies have reached a level of comprehensiveness, throughput and quantitative quality that was inconceivable just a few years back. However, applying proteomics to biological projects still requires lots of knowledge about experimental design, optimal sample preparation, most suitable mass spectrometric technologies and statistical interpretation. If we manage to bring both worlds together and teach biologists about the power, as well as the caveats, of proteomics, I think this will really impact life science in many aspects and truly transform the way how scientific projects are carried out for many scientists all over the world.

JK: I agree. Demonstrating the versatility, and thereby the potential and broad utility of proteomics in different contexts is sometimes an eye-opener for course participants. Actually, it is interesting and useful that participants come from all corners of biology, from paleobiology to clinical biomarker discovery. Having those together in a room for a week and interact, with proteomics as the common interest, is fascinating to see as an organiser. And we explicitly facilitate such interactions in discussion groups – it is an important goal of the course.

5. How do you see this course growing in the future?

CL: I think one special feature of this course, compared to other proteomics courses, is that its rather familial in character due to the small number of 24 participants, and that they come from purposefully different countries and research institutes. This rather small group size is optimal in terms of group dynamics and allows lots of personal exchange between participants and speakers, as well as an optimal support during the practical sessions. Therefore, I hope also in the future the small and familiar atmosphere of this course will remain.

JK: What I also hope, and what we’ll try to achieve, is to remain up-to-date and include novel technologies that are emerging. After 20 years of steep development in mass spectrometry, one would expect that this levels off at some point, but this is not the case at all – it is actually difficult to keep up with what is happening, and with what is possible today that you would not dare to think about yesterday. Therefore, a remaining goal for us is to invite speakers and trainers who work at the forefront of technology, but who can also bridge this to important biological applications. This is what excites us as organisers, and we hope that this will help to make this one of the courses to go to for younger generations of scientists, and get infected too.

6. What motivates you most about your work?

CL: What I really love about heading a proteomics core facility is the huge variety of cool scientific projects you get exposed to, as well as the fact that you work closely with lots of very different scientists coming from completely different scientific disciplines. Every project and every collaboration partner challenges you in terms of diving into a new research area, providing an optimal proteomic workflow and also teaching and educating your collaboration partners in understanding their proteomic data.

MS: The fact that you have the constant possibility to come up and implement creative ideas is incredibly rewarding. Also the fact in research you are constantly generating results that are the first of their kind. There is always an experiment done that has not been done by anyone before and you are the first to see the results. I also love the academic environment the freedom and craziness of it all.

7. Why did you end up in the field of Proteins and Proteomics?

CL: Already during my Chemistry studies all the “biochemistry” lectures and practicals that focused on proteins and life sciences were by far the most interesting subjects for me. During my PhD, which I did in the field of protein engineering at the TU Dortmund, I studied a specific class of proteins, so called inteins, but I hardly applied any mass spectrometry during that time. However, for one specific experiment I used for the first time MALDI-MS to identify the reaction products of a set of purified inteins. My MALDI measurements showed the occurrences of an unexplainable loss of 18 m/z for one of my inteins. First I thought I did a mistake and was very frustrated. But when I repeated and further investigated my samples using also ESI tandem mass spectrometry I could proof the existence of a very interesting cyclic protein-intermediate, which actually helped me explaining the underlying protein splicing mechanism. This turned out being the most interesting result of my whole PhD.

MS: I originally was very focused on pure mathematics. By chance I had an encounter with Roman Zubarev who was a new professor at Uppsala University at the time. His drive, energy and passion for science convinced me to switch fields from mathematics to mass spectrometry and proteomics, which I never regretted.

8. What could you not do without in your life?

CL: Well, as a mother of two beautiful kids the very first thing I could not do without in my life is of course my family :)! And together with my family we love being outdoors, ideally in the Alps, either on (mountain)bikes, rock climbing or hiking. Living without mountains and outdoor activities would be very hard.

MS: First and foremost, my family! Second is physical activity. I love science and I love working a lot, but it takes its toll physically and mentally. My perfect way of recovering and getting the energy back is ideally by rock climbing, running and being out in nature in general.

9. If you would get the chance to meet a famous person – no matter if this person is still alive or not – who would that be?

CL: As a hobby climber I would really like to once meet Alex Honold, who is a world famous free-solo climber who climbed many of the most difficult and exposed climbs in Yosemite National Park without rope. Alex seems in interviews and videos like a really nice and funny guy, but I believe his brain must function very differently than mine when it comes to fear of height, so I would love chat with him about that ;).

MS: I was always interested in mathematics as well as computer science. It would have been fascinating to meet Alan Turing and discuss his vision of how things would develop based on what he knew back then. Incidentally, he was also a really excellent long distance runner with sub 3 hours’ marathon times. It would have been exciting to have a discussion over a run on the countryside :).

10. Which was the best decision in your career so far?

CL: I think the best decision for my career was to perform my Postdoc in the group of Professor Ruedi Abersold at the ETH Zürich, because this has really been the door opener for my career so far. When I finished my PhD it was actually not easy for me to decide for a postdoc in the field of mass spectrometry, because I hardly had any MS experience (I only performed this one MS experiment that I already described above ;)). And starting in a proteomics expert lab as a postdoc who had never really done proteomics before was definitely not easy in the beginning. But I did learn a lot of new things fast and ultimately this allowed me to bring together the two different expertises from my PhD and my Postdoc, which I do believe is a big advantage for any scientific career.

MS: Professionally, I think doing PhD in mass spectrometry was probably the best decision I have made so far. That early in your career, one still knows very little of the world and some luck is definitely required.


Interested in this course? Apply by 22 March!

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Meet the Trainer – Paolo Ronchi

PHOTO: Paolo Ronchi

Meet Dr. Paolo Ronchi, scientist in the Electron Microscopy Core Facility (EMCF) at EMBL, which helps users answer their biological questions by developing strategies and workflows.

Paolo first joined EMBL in 2008 as a PostDoc to study  the biogenesis of the Golgi apparatus after removal of this organelle from living cells by laser nanosurgery. 

Why did you choose to become a scientist?

During my studies, I was always more interested in literature and philosophy. However, when I had to decide for a university subject, out of curiosity I opted for something different: a new biotechnology course had just been opened and I enrolled. Despite this accidental start, I now think that a scientific career has been a good fit for my critical and curious mind.

Where do you see this field heading in the future?

It is very difficult to foresee where the developments are going to bring us. A few years ago, due to the developments in fluorescence proteins and light microscopy techniques, probably not many people would have bet on a bright future for electron microscopy (EM). Now the field is more active than ever, with 3D EM and correlative light and electron microscopy being key to new discoveries in biology. In the near future, I am convinced that the goal of the EM community should be to advance our methods (from sample prep to image analysis) to a higher throughput, to finally make EM a quantitative tool.

How has training influenced your career?

Working in a facility and being highly involved in training, I  experience daily how important courses are to disseminate knowledge and network with a community of experts. Furthermore my personal experience shows how attending a course can change your career, even many years afterwards. At some point during my PhD studies I realised I needed to perform some EM experiments. Therefore, I applied to the course on “Electron microscopy and stereology in cell biology”. It was a great experience, I learned a lot and, when I went back home, I could finally carry out the experiment that was missing for my thesis. In addition to this, I got to know many electron microscopists, including Yannick Schwab, who was a student of the course that year. I do not know whether the good memories of  that time played a role in getting me a job when, 10 years later, I applied for a position in the EMCF at EMBL (which Yannick is now heading),  but for sure it helped my confidence to start a new job.

What is your number one tip for people looking for scientific training?

Even though nowadays you can find all kind of tutorials online, I believe that attending a course in person is still key because of the networking possibilities that it gives. Getting the best experts to sit with you and think about your questions and problems is incredibly valuable. And when you go back home, you will remain part of a community that is in touch to share experience and tips.

If you weren’t a scientist, what would you be?

A professional cyclist  🙂

You are organising the EMBO Practical Course “Advanced Electron Microscopy for Cell Biology” (16 – 26 June 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

I think this course is really unique in many aspects. First of all, hands-on practicals are not just demos by the experts, but the students also have the possibility to learn using their own samples. In addition, the almost 1:1 ratio between students and trainers gives everybody the chance to be trained individually at the level they need. It is not by chance that many leading electron microscopists of today have attended this course in the past.

Interested in this course? Apply by 24 March 2020.

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Meet the Trainer – María del Mar Vivanco

PHOTO: María del Mar Vivanco

Meet María del Mar Vivanco, Team Leader at CIC bioGUNE in Bilbao, Spain. Maria is one of the organisers of the EMBO Practical Course: Techniques for Mammary Gland Research (1 – 6 March 2020).

What is your research focus?

I am interested in cancer heterogeneity, why some cells respond to therapy while others do not, thus contributing to development of resistance and metastasis. In particular, I am intrigued about the complex effects of transcription factors, which are required for normal physiology of the mammary gland and are also implicated in tumorigenesis and development of resistance to therapy in breast cancer.

Why did you choose to become a scientist?

When I was young I had a variety of interests – psychology, physics, art, biology… However, I was intrigued by science and anything related to DNA and its regulation. Then I did my PhD at EMBL Heidelberg (Gene Expression Programme) and discovered the opportunities in research for identifying problems, looking for solutions and the thrill of finding some of the answers…and I was hooked!

Where do you see this field heading in the future?

Despite significant progress in cancer research and clinical advances, breast cancer still is the most commonly diagnosed cancer – one in eight women will develop this disease during their lifetime – and it claims the lives of more women than any other cancer, plus men can also get breast cancer. This highlights the unmet clinical need for improved strategies for prevention, early detection and more efficient and specific treatments in order to accelerate progress and help more patients survive the disease.

One of the features that characterises breast cancer is its heterogeneity, both among patients and within each patient tumor. This heterogeneity is found at molecular, phenotypic and functional levels, complicating diagnosis and challenging approaches to therapy. Currently, huge efforts are dedicated to understanding this heterogeneity at all levels, including at single-cell resolution, which is anticipated to open new possibilities for more efficient and specific anti-cancer therapies.

How has training influenced your career? 

Doing my PhD at EMBL marked the way I envision science, and this vision was reinforced and developed further at UCSF. Science can – and SHOULD – be fun. Later on, funding struggles and the current publishing madness have somehow taken a toll on the fun element, so I just have to remind myself sometimes that science is still exciting!

If you weren’t a scientist, what would you be?

An artist.

You are one of the organisers of the EMBO Practical Course: Techniques for Mammary Gland Research (1 – 6 March 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

Some of the techniques practiced at this course are specific for the mammary gland and thus it provides a solid base for researchers starting in this field. In addition, there is a significant emphasis on imaging and comparison of mouse and human studies, the two major systems for looking at normal physiology and cancer research that, when combined, offer great insights into this heterogeneous disease. In addition, having the opportunity to work alongside other trainees contributes to the establishment of a network that may be helpful in the future. Cancer is a very complex problem, and having collaborators with different views and expertise will be very useful in your career.

Interested in this course? Submit your application by 8 December!

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Meet the Trainer – Pavel Baranov

Meet Pavel Baranov, Professor of Biomolecular Informatics at the University College Cork, Ireland. Pavel’s research group focuses on the understanding of how proteins are synthesised and how their synthesis is regulated.

Why did you choose to become a scientist?

When I was a toddler, I wanted to be a firefighter. Within a couple of years, I decided that being an astronaut would be more fun. A few more years passed, and I began to dream of becoming a scientist. I guess at that point I stopped growing and started living my dream.

What is your research focus?

My research group studies RNA translation. Translation is at the core of biology. Cells spend most of their energy on protein synthesis and the ribosome is the most abundant molecular machine in almost all cells. Ribosomal RNAs and tRNAs are the most conserved molecules across all kingdoms of life, and it is now apparent that proteins evolved earlier than DNA. Life as we know it relies on two main type of molecules not found outside of living systems – nucleic acids and proteins. It is the process of translation that connects these two chemistries together. I could hardly think of a more fundamental, interesting and challenging cellular process than translation.

Where do you see this field heading in the future?

As translation brings two chemistries together it is far more complex than other molecular process such as transcription and replication. Because of its complexity and the lack of tools to study it, studying translation is very challenging. The tools are now being developed, e.g. variations of ribosome profiling techniques, real-time single molecule imaging, cryo-EM microscopy, etc. The main change that I foresee is that translation will draw the attention of many more biomedical researchers, for better or worse.

What is your number one tip for people looking for scientific training?

Independent practice is the key in my opinion. After taking a course you may get the impression that you can do something, but it could be a false impression – you don’t really know if you can unless you have done it.

If you weren’t a scientist, what would you be?

Science is not a job for me, it is a dream. If I were not able to make my living as a researcher, I would have to find something else to make earnings, but I would not give up on my scientific interests.

You are organising the EMBO Practical Course ”Measuring Translational Dynamics by Ribosome Profiling” (3 – 9 May 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

The invention of ribosome profiling is the most significant development in the field of protein synthesis since the deciphering of the ribosome 3D structure. Ribosomal profiling is a popular technique for measuring the rate of translation in addition to measuring RNA levels, but this was somewhat possible even before. The unique ability of ribosome profiling is the detection of which open reading frames are being translated in RNA. The application of ribosome profiling revealed that even in eukaryotes the same mRNA molecule is often used for making more than one polypeptide, and that our current knowledge of the human genome protein coding repertoire is still far from complete. In addition to detecting translated frames, ribosome profiling could be used to detect ribosome pauses.  We recently learned that such pauses could be used to regulate gene expression and other biological processes.  This course will provide trainees with everything what is needed for mastering this powerful technology, from hands-on experience in generating ribosome profiling data to bioinformatics analysis and the use of public data resources.

Interested in this course? Submit your application by 9 February!

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Meet the Trainers – Raffaele Calogero, Jeroen Krijgsveld, Lennart Martens

This month we have not one but three trainers we would like to introduce you to. Meet Raffaele Calogero, Jeroen Krijgsveld and Lennart Martens, organisers and trainers at the EMBL Course: Analysis and Integration of Transcriptome and Proteome Data (2 – 7 February 2020).

What is your research focus and why did you choose to become a scientist?

RC: I have a background in molecular biology, but since 1999 I have been working in transcriptomics data analysis and tool development. I became a scientist because I loved the idea of investigating new unknown topics every day.

LM: My research focus is bioinformatics, which stems directly from becoming completely taken in by computers at an early age. Like many of my generation, I started out with a Commodore 64 when I was 8, and had written my first (very, very simple :)) program in BASIC after two weeks. But my link with science came about after I stumbled across an episode of Jacob Bronowski’s ‘The Ascent of Man’ a few years later (I think I was 10 or 11) on Saturday morning on television, and this inspired a lifelong interest in anything scientific. All in all, I consider myself extremely lucky to be able to combine my passion for computers with my passion for science, and make a living out of it!

JK: My research focus is on proteomics, where we develop and apply mass spectrometry-based technologies to understand the intricate machineries used by cells to respond to their environment. Curiosity to understand how things work is as an important motivation for our current research as it was for me during my studies. Becoming a scientist has always felt a natural path for me to follow, and I have never seriously considered doing anything else. Although at the same time, when looking back, I realise how fortunate I have been being given the opportunity to follow my interest and move between fields. This is due in no small part to having training opportunities and stimulating environments at the various stages of my career!

Where do you see this field heading in the future?

RC: Data integration is the new upcoming frontier for biological studies, and transcriptomics and proteomics are going to be important players in the game.

JK: Proteomics has come a long way in the last 2 decades, reaching its current ability to characterise thousands of proteins in a single experiment, and do this across multiple experiments. I expect that during the next 5-10 years we will see how these investments will pay off, helping to understand processes at the protein level very similar to the way this has been achieved in genomics. After transitioning from a technology exclusively for physicists to a useful tool used by biologists, the next big step to be made is to implement mass spectrometry in the clinical arena. Integration with genomic methods and data types will be key to drive this forward.

LM: Bioinformatics is slowly taking over much of large-scale biology. Of course, focused biochemical and molecular biology research will remain the staple of the life sciences, but our ability to process and interrogate very large amounts of (potentially even heterogeneous) data is transforming our ability to generate new leads, new ideas, and to shed a much more holistic view on life at the molecular level. And with the advent of extremely powerful parallel computing, the field of machine learning has received an enormous boost, further increasing our ability to spot previously hidden patterns in our data. So it’s an exciting time in bioinformatics, with lots of new areas of research opening up to us for the first time! We’re going to continue having a lot of fun for a long time!

How has training influenced your career?

JK: This has been fundamental, in different ways. One is in a formal way, where classes and courses have been key to shaping a foundation, and helping to fill specific knowledge gaps. The second is less formal, which to me has been at least equally important, where I got trained by working in different research environments together with people of different backgrounds.

RC: In my role as an associate professor, training is part of my everyday life. I am involved in many advanced courses through my university, both in Europe and in Asia, and I think that courses are useful for both participants and instructors. The former grab the knowledge from the latter and the latter get new fresh view points from the former.

LM: Many of the excellent teachers I have studied with have left a deep impression on me, and guided my career path indirectly. As to providing training, it is one of the aspects of my job that I most cherish. For me, the importance of sharing and spreading knowledge resonates very closely to the core principles of science: by sharing and exchanging knowledge, all participants in the teaching experience gain something. In all, the biggest contribution that training has had to my career, is in greatly enhancing my ability to be creative in a productive way.

What is your number one tip for people looking for scientific training?

LM: Go for it, and seek out courses taught by those rare experts that both intimately know their field, but can also clearly communicate about the essence of that field. You don’t want to only grasp the current ‘hot’ method at a user level, but rather want to understand how that field works, how it has evolved, and how the current methods fit in with this. Courses that focus on these aspects deliver knowledge that lasts for much longer!

JK: It is two-fold: find a course that gives you the theoretical foundation of an area or topic you would like to venture into. After this, I think it is essential to ‘internalise’ this knowledge, so I would advise you to find a collaborator or colleague to help you along the path to use the acquired knowledge. It is like driving a car: you need to get a driver’s license to be allowed on the road, but you really learn how to do it by practicing afterwards.

If you weren’t a scientist, what would you be?

RC: Definitively a Medical Doctor.

LM: Most likely a software developer or systems architect of some sort. I worked in industry for a few years after my Masters degree, and then chose to pursue a PhD rather than take a very nice position at Microsoft. So if I had made a different choice then, I’d probably still be in IT!

JK: I have never really been in a situation where I had to choose between being a scientist or do something else, but thinking about it now I would like to think I would be a writer, a novelist. The reason is that I like writing, and it is part of my every day job, however writing papers and proposals comes with a lot of constraints and requirements. Making up stories without the boundaries of page limits, allowing fantasy and imagination, in an expanded vocabulary and, above all, in my mother tongue sounds all very appealing to me. Maybe one day. 🙂

You are organising the EMBL Course: Analysis and Integration of Transcriptome and Proteome Data (2 – 7 February 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

JK: The greatest benefit is that it allows participants to have a look ‘over the fence’: most participants usually have a background either in genomics or proteomics, and being exposed to both aspects – along with the technologies and methods used in these fields – allows them to ask questions they may not have thought about before. What we try to achieve is that they could even go a step further, and integrate the new knowledge in their research to gain a more complete picture of the biological systems they are using.

LM: The course is unique in that it brings together the two key fields of research to understand cellular functional: transcriptomics, which traces the usage of the information in the genome in a given cell, and proteomics, which shows the actual biochemical and signalling capability of a given cell. There is important information at each of these levels, and these are moreover more complementary than many might think.

Of course, gene regulation provides important insights into a cell’s internal processes, but proteins are not only made or broken down, they are also closely regulated at the protein level. A complete picture of a cellular process thus requires insight into (and thus data from) both the gene expression level as well as the protein level. This is where this course provides the right skills for researchers; teaching them how to integrate data from their transcriptomics and proteomics experiments.

The usefulness for the bigger picture is therefore more or less implicit: by combining transcriptomics and proteomics, a much more complete picture of cellular functioning can be obtained. And let’s be honest, isn’t that what all of us really want to obtain, after all? 🙂

RC: I think the phrase of Claudia Manzoni in the abstract of her paper in Briefing in Bioinformatics in 2016 (Volume 19, Issue 2, March 2018, Pages 286–302) “Our work intends to target students and researchers seeking knowledge outside of their field of expertise and fosters a leap from the reductionist to the global-integrative analytical approach in research” is a perfect explanation for our course.


Interested in this course? Apply by 10 November!

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