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Stefan Loroch - Travel Grant Report
Annual Conference of the American Society for Mass Spectrometry 2016
San Antonio, Texas, USA (June 4th-9th)

My name is Stefan Loroch, I am a PhD student at the Leibniz-Institut für Analytische Wissenschaften - ISAS – e.V. in Dortmund, Germany. I am focussing mainly on the development and application of proteomics and phosphoproteomics methods for clinical research.

Fortunately, I had the opportunity to attend the ASMS 2016 in San Antonio Texas with a DGPF travel grant. The ASMS annual conference is one of the biggest conferences in the field mass spectrometry and therefor a perfect place to meet scientist from all over the world for a vivid exchange. Consequently, it was a perfect opportunity to present my results to other scientists and PhD students. The feedbacks for my poster were quite positive and I established several contacts to researchers interested in establishing my presented methods. The exchange with other researchers during the poster sessions (16 hours in total over 4 days) is in my opinion an absolute highlight!

The key-note-lectures were a great opportunity to gain deeper insights into various mass spectrometry-related topics. I enjoyed learning about the developments of ionization techniques in the past decades (Lars Konermann, University of Western Ontario, “An Analyte's Journey from Solution into the Gas Phase”) and developments in fragmentation techniques (Kristina Håkansson, Biemann Medal Lecture, University of Michigan). Both lectures were highly interesting overviews about key-studies in the field and provided deep insights in what really happens to ions in a mass spectrometer. Besides, the two-day workshop “Glycans and Glycoproteins in Mass Spectrometry” was an excellent introduction to glycan analysis methods developed over the past decades.

In summary, I am very glad that the DGPF gave me the financial support necessary to participate in this conference. I hope to get the opportunity to participate again in the next years.

Report on the EuPA 2016 (22-25th June 2016) by Phillip Ihmor

The EuPA 2016 conference was this year’s highlight for every European proteomics researcher.  It was hosted by Prof. Aysel Ozpınar on the brand new campus of the Acibadem Medical University in Istanbul, Turkey. This annual congress of the European Proteomics Association - inspired by its host city's heritage - brought East and the West together to facilitate in-depth scientific exchange.

Over four days, the conference was filled with exciting talks of the newest developments of all areas of the vast proteomics field.  There were talks on massive scale scientific endeavors for instance by Prof. Samir Hanash on super-large cohorts studies for cancer biomarkers, or Prof. Fuchu He mapping the human liver proteome, or by Prof. Peipei Ping on getting true knowledge from the bioinformatics big data deluge. Also emerging niche topics like ion mobility mass spectrometry, glycosylation studies, middle-down proteomics, multi-PTM studies or imaging mass spectrometry for the clinics were presented.

The conference’s organizers went to great lengths to balance the presentation opportunities for established senior scientists with their long and broad perspectives with the ingenious and novel approaches of young researchers. For me, these shorter talks maybe even shared the more exciting approaches and ideas. Especially, the talk of Dr. Fan Liu of Albert Heck’s lab on XlinkX 2.0 was well received and got her awarded with the conference's Young Investigators price. XlinkX 2.0 is an improved search engine to identify cross linked peptides for structural biology approaches.

The conferences was centered on the motto of "Challenge accepted: Standardization of Proteomics". Especially the preceding workshops addressed this issue, which we as a profession as a whole have to face. It was highlighted that these challenges are not just during one step of the analysis, but go along the whole pipeline from the experimental design, to the sample preparation, the MS measurement and finally the bioinformatics interpretation. All these steps have to be validated, benchmarked and standardized to create insightful science.

Such issues were also highlighted by Prof. Lottspeich, the author of “Bioanalytik”, the most renowned textbook that sparked my personal passion for mass spectrometry. He was awarded the Juan Pablo Albar price for his lifetime achievements in the field. In his lecture, he guided the audience through the rich history of proteomics and relentlessly showed both the strengths and weaknesses of our approach. He clearly stated the need for more robust standardization and called for all young researchers to break through the hype and to deliver on our promises.

With these honest words, Prof. Lottspeich summarized this year’s EUPA conference perfectly. There are great challenges ahead of us, which we can tackle when brought together especially in such a friendly and open atmosphere like the EuPA 2016. The sharing of crucial information both on stage and besides it, gave me confidence that we together can grow further. Especially with the political turmoil in Turkey shortly after the conference ended, I think I can speak for all attendees that we stand together with our new Turkish friends and we are looking forward to your contributions to future conferences. Stay safe.

Viviana Greco
Proteomic Forum 2015 (22. - 25. März 2015)

It was a great opportunity for me to participate to the Proteomic Forum 2015 where progress and new technologies in several fields of proteome research and application have been showed. The first day was dedicated to educational program and EuPA initiative; I followed the last one for my involvement in the EuPA organizing committee 2015. In the next days, the program was organized in different sessions and it was covered several areas, from New Technologies to  Extracellular Vesicles and Subcellular Proteomics, from Post-Translational Modifications and Structural Proteomics and Computational Omics to Plant and Agricultural Proteomics, Microbial Proteomics and Antibiotical Resistance to Disease Proteomics.

The presence of so important speakers (among these M. Mann, R. Aebersold, C. Overall and many others)  was represented the possibility for me to deepen my skills and to further improve my knowledge regarding proteomics tools. Furthermore, this surely increased my enthusiasm for research in proteomics field. Moreover, three poster sessions, so well organized, provided not only the opportunity to present the latest results from our studies, but also a great opportunity to promote exchanges and collaboration , especially among our young researchers.

Sincerely,
Viviana Greco


Stefan Loroch
HUPO World Congress 2014 in Madrid, Spain (October  5th-8th

My name is Stefan Loroch, I am a PhD student at the Leibniz-Institut für Analytische Wissenschaften  - ISAS – e.V. in Dortmund, Germany. I am focussing mainly on the development and application of proteomics and phosphoproteomics workflows for clinical research.

Fortunately, I had the opportunity to attend the HUPO World Congress 2014 in Madrid with a DGPF travel grant. I had chosen this conference since the scientific program perfectly met my field of research and interest. The lectures were focussing on various proteomics sub-disciplines often with clinical relevance. Thus, it was ideal to expand my knowledge about my own and related topics. Especially the key-note lectures were a great opportunity to gain deeper insights in the development of proteomics in the past decade and in the context of the related disciplines genomics and transcriptomics.

It was a perfect conference to present my results to other scientists and PhD students. Fortunately my abstract was chosen for an oral presentation in the phosphoproteomics session, so I had the great opportunity to give a talk in front of a large scientific audience. The feedbacks after were very positive and I could establish contacts to other phosphoproteomics specialists and people that were interessted in establishing techniques I have presented.

During the social event I met other PhD students from all over the world and was introduced to some of the “big guys” in my field. I really enjoyed to talk to the scientists I only knew from the papers so far.

In summary, I am really glad that the DGPF gave me the financial support necessary to participate in this conference. I hope to get the opportunity to participate again in the next years.

 

University of Bergen, Norway - Sebastian Hesse

My name is Sebastian Hesse, I am a physician scientist working as a postdoctoral fellow at the laboratory of Prof. Christoph Klein at the Haunersche Kinderklinik, LMU Munich. My main research topic is the proteomic profiling of neutrophil granulocytes. The DGPF supported my participation of a course in “Bioinformatics in Proteomics” at the University of Bergen, Norway (12. – 15. May 2014)

The course was a unique opportunity to learn directly from the developers of the most commonly used software solutions in proteomics (SearchGUI and PeptideShaker). The team at the PROBE center (Proteomics Unit University of Bergen) around Prof. Dr. Frode Berven was incredibly dedicated to teach a small group of participants every aspect of the bioinformatic analysis of raw proteomic data, ranging from the right experimental setup to first data overviews, protein identification and targeted as well as untargeted quantification. The software covered in the course was: SearchGUI, PeptideShaker, MaxQuant, Perseus and Skyline.

The days were very nicely organized and offered a perfect mix of background information delivered through lectures and direct hands on calculations every participant had to do on its own. During every practical session a group of teachers was around to explain any upcoming question. I felt very secure and could solve every question that came up regarding my own project.

Additionally there were two social events where the participants could meet and exchange ideas freely. All was very well organized and you could feel the dedication of the organizers to make this a unique experience for the participants.

This course was a unique opportunity for me to really get involved into the data processing of proteomics. I am very confident that this course now enabled me to set up my project right and to be aware of most of the pitfalls in proteomic data analysis. I highly recommend this course to everyone working in a proteomics based project (http://www.uib.no/en/rg/probe) and would like to express my gratitude to the DGPF for supporting me to participate at it!

Sebastian Hesse, MD

 SUMMERSCHOOL BRIXEN 2013 - Christian Moritz

My name is Christian Moritz and I’m Postdoc at the University of Kaiserslautern. After finishing my doctoral thesis some months ago, I now took the chance to join the summer school "Advanced Proteomics 2013". My motivation was to present my newest results, to deepen my proteomics knowledge and to meet people from the same research field.

The summer school was one of the best scientific meetings I ever joined. The intriguing location – the Novacella monastery in Brixen/Italy – offered inspiration for learning new things and meeting new people. I really enjoyed the very international character of the summer school. Some students even took a trip from Brazil or South Africa to join the school, which speaks for the high quality of the event.

The days were structured very well. The mornings were used for lectures – one basic lecture and two research lectures. Fortunately, the quality of these contributions was higher than at other scientific meetings. Nevertheless, I was once more surprised about the missing didactic skills of a few scientists.

The afternoons offered workshops. Albeit the name "workshop" was a bit inappropriate in some cases, these events allowed to interactively deepen and broaden a topic. My favourite workshop was that of Thierry Rabilloud, who charmingly answered our questions on sample preparation.

Definitely worth mentioning are the social events. Rafting, mountain hiking and wine tasting turned the group of international and interdisciplinary individuals into a great and harmonic team. Further, I don’t want to miss mentioning my first open-air poster session, which even resulted in a poster prize for me. Another successful moment was my header goal, by which I could beat the great goal keeper Henning Urlaub during our amusing soccer match :-)

I really enjoyed the days in Italy. Thanks to the organizers! I met lots of potential cooperation partners as well as new friends.

 

ASMS CONFERENCE 2013 in Minneapolis - JULIET PADDEN

My name is Juliet Padden and I started as a PhD student in the Medizinisches Proteom-Center in Bochum at the beginning of 2012. I am a member of the research group Clinical Proteomics headed by Jun.-Prof. Barbara Sitek where I work on the discovery of novel protein biomarkers for cholangiocellular carcinoma, also known as bile duct cancer.

This year in June I visited the ASMS conference in Minneapolis benefiting from a SOGS travel grant. This is a huge mass spectrometry conference with almost 400 talks and over 2,700 poster presentations.Prior to the actual conference I participated in a two-day workshop about metabolomics, a field we have recently started to work on in our lab. For me as newcomer to this topic it was very helpful because the speakers focused on the basics of metabolomics and provided some protocols for sample preparation and method development.

The oral sessions of the conference whichwere overall of very high qualitycovered a large range of different topics and the overwhelmingly large poster sessions led to many fruitful discussions. These gave me new ideas for my project and resulted in a potential future collaboration.

Since the experiments of J. J. Thompson in the year 1913 are considered to mark the beginning of mass spectrometry, the ASMS 2013 celebrated 100 years of mass spectrometry with interesting talks and posters about the history of MS as well as an MS “museum” displaying historical instruments and accessories. Furthermore, every participant received a free reproduction of J. J. Thompson´s 1913 edition of “Rays of Positive Electricity”.

Another highlight at the ASMS was visiting the corporate hospitality suites where companies presented their latest innovations in a relaxed atmosphere with free drinks, food and a lot of entertainment. This was the perfect opportunity for discussions about technological and methodological issues and for socialising with other participants as well as company representatives.

For me, the ASMS is a very impressive conference which serves as a rich source of information and ideas and gives scientists from all over the world a chance for networking. I therefore hope to get the opportunity to visit this congress again in the future.

SUMMER SCHOOL BRIXEN 2013 - STEFANIE SAWADA

My name is Stefanie Sawada and I am working at the Federal Institute for Risk Assessment (BfR, Berlin) in the department Food Safety. My PhD project focuses on the proteomic analysis of adverse health effects of the food processing contaminants 3-MCPD and its esters (dipalmitate of 3-MCPD) in rat target organs liver, kidney and testis.
I participated for the first time at the summer school – Advanced Proteomics – which took place in Brixen. The venue was very special because it was located at the Monastery of Neustift. Besides basic proteomic lectures it was possible to take part at diverse workshops. In my opinion the SRM workshop with Christina Ludwig was one of the best. At the end of this course we played SRM jeopardy and could test the acquired new knowledge. Furthermore, I liked the talk during the poster presentation. Especially from Thierry Rabilloud I got helpful suggestions for ongoing research. At one afternoon when there were no lectures, all participants were hiking from the Zanser Alm to the Schlütterhütte (see picture). This trip was a good opportunity to get to know other participants as well as the speakers.
In summary, I enjoyed the summer school very much. The lectures covered the wide field of proteomics and were quite instructive. Many international speakers and company representatives stayed at the monastery the whole time and were prepared to respond to questions. Moreover, this event was a great chance to get in contact and share experiences with many other PhD students using proteomic approaches.

SUMMER SCHOOL BRIXEN 2013 - SARA GALOZZI

My name is Sara Galozzi and I am PhD student in the department of Functional Proteomic in the Medical Proteome Center, Ruhr University of Bochum, Germany. My project aims to investigate a mass spectrometry based quantification method for biomarkers in Alzheimer’s and Parkinson’s diseases.

I participated in the 7th European Summer School “Advanced proteomics” in Brixen (Italy) from 04.08 – 10.08.2013. The talks were interesting and the speakers were renowned experts in the fieldof proteomics. I had the opportunity to present and discuss my results in the poster with other PhD students and researchers. Coming from all over the world, there were more than seventy participants. I took part in three workshops where the tutors presented an introduction to the topic, followed by a practical exercise. Since I am going to use SRM method,the workshop about it was really helpful. There were various experts from different companies in the school and they presented new mass spectrometers. I had the opportunity to enquire their offers and suggestionabout mass spectrometer setup.

We also had some sports activities: hiking tour in the dolomites and rafting! The school was in a beautiful monastery, in which I not only enjoyed the landscape but also the food. In the last evening, we had a wine tasting lecture taken by a sommelier.

The 7th European Summer School “Advanced proteomics” 2013 in Brixenwas a great scientific and social event. The school waswell organized and I was very pleased to attend and I am very much thankful to the DGPF for the travelling grant.

Proteomic Forum 2013, Berlin, Nadine Dyballa-Rukes

My name is Nadine Dyballa-Rukes and I applied for the Research Travel Grant of the DGPF to attend the Proteomic Forum 2013 in Berlin. I am currently working on a proteomics-based project for Professor D’Haese at the Heinrich-Heine University. Using two-dimensional gel electrophoresis and mass spectrometry I investigate the diversification of the actin-binding protein CapG in its expression pattern.

The goals that I set before attending the Proteomic Forum 2013 were as follows:

  • update myself on the latest developments in proteomics technologies
  • get alternative analytical strategies to analyze my data set
  • attend informal sessions to discuss individual open questions with experts in the field

My participation met all of these goals.

The conference started for me on Sunday, the 17th March, with the Doctor’s Office about 2D electrophoresis. It gave me the opportunity to discuss actual gel-based issues and best practices with colleagues, and Rainer Westermeier as expert in the field. I got further access to experts in the News Corner session that shared results and developments in a particular technology (mainly from companies). The educational value of the Proteomic Forum was completed by attending the open round table discussion in the Doctor’s Office about mass spectrometry.

I also joined the SoGS-Stammtisch on Monday night at Luise Restaurant. It really was a great experience to get in contact with the experts during beer and wine. For example I had a stimulating talk with Roland Kellner about working at the university and in the pharmaceutical industry. This discussion was extremely fruitful to me as I am now at the point where I have to decide whether I continue protein analysis at a scientific institution or cross industry lines.

Each day started with a handful Plenary Lectures of local and national speakers. It is always fascinating how well-known personalities from leading proteomics institutions present coherent approaches and tools to elucidate protein inventories to assign functions, apply proteomics to issues in human health, biology and biotechnology ending with efforts to understand protein function and systems biology to put results in a broader context.
During the Symposia I could discover best practices from experts in the respective field of quantitative proteomics and protein modifications. Here I also heard about how to investigate new ways to look at old problems.

Nevertheless, the most input for my work I received during the Poster Session. It is amazing how casual and at the same time procreative the personal presentation of one’s own data is.

Proteomic Forum 2013, Berlin, Jennifer Geddes

My name is Jennifer Geddes and I am a PhD Candidate at the University of British Columbia in Vancouver, Canada. My project focuses on characterizing the proteome of the human fungal pathogen, Cryptococcus neoformans, in response to cAMP/Protein Kinase A signaling.  Specifically, I am interested in the secretome, cellular proteome, and phosphoproteome.

This was my first year attending the Proteomic Forum and I thoroughly enjoyed the meeting. The plenary sessions were informative, featuring internationally renowned researchers, and appealed to a wide audience. These sessions were an excellent opportunity to hear from leaders in the field of proteomics and to initiate substantial discussion during the coffee breaks. The size of the conference was ideal and provided many opportunities for networking and meeting fellow graduate students, along with prospective post-doctoral supervisors. The concurrent sessions were very well organized and covered a broad range of topics, and provided students with an opportunity to share their research.

This was my first visit to Berlin and so I appreciated the free afternoon on Tuesday to view the city and visit historical sites along the way. I found the people to accommodating (as I do not speak German) and the pastries to be delicious!

Overall, I was very pleased that I could attend the Proteomic Forum 2013, in part due to receiving a travel award from the DGPF. The caliber of scientists present at the meeting and the international representation made for a very rich experience and I look forward to attending another Forum in the future.

Proteomic Forum 2013, Berlin, Laura Postolache

My name is Laura Postolache and I am currently a PhD student in the Junior Research Group “Biomarker Discovery”, headed by Dr. Christoph Rösli, at DKFZ and HI-STEM in Heidelberg. My work attempts to identify new protein markers for pancreatic ductal adenocarcinoma, which can be later on targeted by antibody based therapies or used for early diagnosis.

This year I became a member of the DGPF and participated  at the Proteomic Forum in Berlin, for which I had received a SoGS travel stipend. For me, it had been a great opportunity to find out important updates in the field of biomarker discovery, with an emphasis on technological improvements. The talks as well as the dinner/lunch conversations helped to shed more light on the strengths and weaknesses of multiple mass spectrometry systems and software tools, information which will be valuable for my future experiments.

I particularly enjoyed the talk of Dr. Dario Neri, whose lab focuses on the development of antibody based therapies. It is sometimes challenging to identify good biomarkers, without targeting or harming healthy organs. His experiments highlighted the importance of testing even biomarkers that are present in healthy organs and would be normally rejected by the common investigator out of fear of causing harm to the patient. His preliminary experiments suggest that no potential good biomarker should be abandoned before performing a full set of tests up to imaging in human.

I also enjoyed the Educational Program lectures, despite the fact that some of them got very technical towards the end. I believe the speakers were highly motivational and the talks offered a good overall and also more detailed insight on their topics.

Since I come from a mixed lab (our group belongs to the division of stem cells and cancer) I was pleased that most of the talks did not only focus on the methodology but also on the chemical/biological application of the presented innovations. In my eyes it is extremely important to bridge the proteomics world with that of the molecular/cellular biologists, since the research field can benefit greatly from strengthen collaborations.

Proteomic Forum 2013, Berlin, Jason Tonillo

My name is Jason Tonillo and I am a PhD student at the Medizinisches Proteom-Center in Bochum, Germany. The focus of my work is the identification of new peroxisomal protein-protein-interactions by affinity purification and subsequent LC-MS analysis.

I participated in Proteomic Forum for the second time. Just like 2011 this year’s Proteomic Forum was well organized. I liked the talks of excellent international speakers and the huge poster sessions although they were crowded. I enjoyed the news corner very much. The mix of short talks from all over the field of proteomics was interesting and informative. Only drawback was the second poster session on Tuesday. It took place simultaneously with the Waters lunch seminar.

During the breaks I took the opportunity to get in contact with company representatives at their booths and to negotiate favorable conditions for products I will order. The catering and the conference dinner were delicious and also suitable for vegetarians. On the free afternoon I explore berlin on my own. Unfortunately it was very cold (about 0 °C) and most museums in berlin close at 5:30.

Proteomic Forum 2013 was a great scientific and social event. In my opinion it is the best conference in Germany to get in contact with international scientists in the field of proteomic.