NewS

HUPOST: Can you tell us what this prize, which is referred to as the Dutch Nobel Prize, means for you, and for the field?

Heck: The Spinoza prize is the most prestigious Dutch science award, and is given annually to three to four researches, selected from all disciplines of science.

It is of course an enormous honour to be awarded this prize, and while it’s known as the Dutch Nobel Prize, it evidently does not compare to the real Nobel. Nevertheless, it comes with a 2.5 million euro budget, to be spend freely for research, so it is a very strong driver for creativity and innovation.

Although a personal prize, I think this award is also an award for my group and the field, because the prize is an implicit recognition for the importance and impact of analytical chemistry, biomolecular mass spectrometry and proteomics.

HUPOST: You have your own Wikipedia page, and a list of prestigious awards to your name. What would be your advice to young researchers who want to make a difference? 

Heck: If you want to make a difference, evidently you should keep up with the literature, so you know what lives in the field, but that knowledge should not stop you from doing the unexpected and you should always look for unexpected findings. In my view, these are the key to innovation and succes. And I try to encourage everyone not to be a follower; try doing something different than the other labs in your field. When you have a keen eye for the unexpected, and do original work, then you will be able to contribute unique findings and can make a difference. And find the right environment, as good mentors are way more important than a good lab-infrastructure.

HUPOST: When a researcher pursues something different, the research can also fail. Do you have any tips on how to deal with such setbacks?

Heck: We should not fear failure. In fact, most scientific experiments end in failure. There’s no satisfaction to be had from planning an experiment for which the outcome is already known. And never forget: after you encounter a few failures, the next success will taste so much sweeter!

HUPOST: If you were a starting scientist today, what topic would you choose?

Heck: My main driver is very broad: understanding how life works at the molecular level. Of course, ‘life’ is very diverse, and there’s much to study. But right now, I would love to look more into how the brain works at the molecular level. This is an area we still understand so little about.

In general, I strongly believe that everybody needs to find something that strongly attracts their interest, as it is very important in science to work on a topic you really care about.

HUPOST: Your lab has also produced very nice short movies to introduce science to the general public; how important is this outreach?

Heck: I think it is very important and exciting to outreach to the general public. But I have also learned that you need to have a strategy for these movies, so that they hit their mark. Importantly, it is also very much fun to make such movies. Overall, I believe that if you study proteins, and are excited about proteins, as I am, that you should also spread this excitement! And because the general public will not read our papers in Nature and Science, such movies are a great way to bring our research to a broader audience. It is particularly rewarding to see that some of our movies are featured in the Washington Post, but these are used in classrooms as well. If you make a movie, try to make them as multi-purpose as possible.

Movie links:

http://www.hecklab.com/molecularclock/

https://www.youtube.com/watch?v=1G6jTGAfgUc&feature=youtu.be

HUPOST: While on the subject of classrooms, do you believe that knowledge about proteomics should move into classrooms?

Heck: Yes, of course, although I would prefer a more overall view: we should be teaching more insight into life at the molecular level in the classrooms, and this should be based on knowledge of the entire cast of macromolecules (DNA, RNA, proteins) that feature in this grand spectacle we call live.

I also think that the progress of scientific knowledge in the life sciences are taking too long to reach the classrooms, and that is a pity. All the more so because the knowledge is so interesting and inspiring. A great example is the gene transcription machinery, which is not only a fundamental process in all life, but it also combines proteins, DNA, and RNA in a fascinating molecular machine.

HUPOST: Which of your contributions to the field gave you the most satisfaction?

Heck: That’s a difficult question. It’s like being asked to pick the favourite child amongst your children. But I really enjoy technology development. This because there is great satisfaction in receiving mails from other researchers that write to let you know that your technology has helped them do their research. Science is all about sharing after all, and when people pick up technologies that you’ve developed, and it works for them, that is extremely motivating.

In addition, new technologies often lead to breakthrough findings in biology. For instance, the EThcD technology we developed has led to the discovery of widespread proteasomally spliced HLA peptides, which shook up the field of immunology. So I really like the ability of technological breakthroughs to lead to a new understanding of biology, which is, after all, the goal!

Paper reference: http://science.sciencemag.org/content/354/6310/354

The MS-Pillar of the Human Proteome Project invites all HUPO members to participate in the Phosphopeptide challenge. The MS Resource Pillar has partnered with SynPeptide Co. Ltd in Shanghai (www.synpeptide.com) to develop a complex set of human phosphopeptides (Ser, Thr or Tyr) singly and multiply phosphorylated) and their unphosphorylated counterparts that can be used for method development and verification for phosphopeptide enrichment, sequence analysis by mass spectrometry and bioinformatic evaluation. The first stage of this initiative is for interested members of the HUPO community to obtain a set of the peptides and apply their own methods and bioinformatic analysis to fully characterize the peptides as a neat mixture and in a tryptic digest background. As a result of this collaborative endeavor, multiple purification schemes, analytical protocols and data processing strategies will be evaluated, making it possible to determine the approach(es) that provide the highest coverage of phosphopeptides in the mixture.

By partnering with SynPeptide the peptide sets are being provided free-of-charge to all HUPO members, with the understanding that the analytical and data processing methods and results will be returned to the MS Resource Pillar committee so they can be collated and reported at the HUPO 2018 meeting. Free aliquots of the peptide mixtures can be obtained at the HUPO2017 Congress in Dublin from Peter Hoo from the SynPeptide stand. MS-Pillar Chair Prof. Sue Weintraub will make a short presentation on Monday September 18 at 16:30.

The Human Proteome Organization (HUPO) and Prof Steve Pennington, UCD, chair of the organizing committee of HUPO2017 (the 16th HUPO World Congress) in collaboration with the National Cancer Institute’s (NCI) International Cancer Proteogenome Consortium (ICPC) announce that they will host a HUPO2017 Global Leadership Gala Dinner on Saturday 16th September. The event is catalyzed in part, by the Cancer Moonshot initiative. The organizers are delighted that the 47th Vice President of the United States of America Joseph R. Biden Jr. will deliver a keynote address at the dinner on the theme of “International Cooperation in the Fight Against Cancer.”

The evening dinner event being held in the Royal College of Physicians in Dublin will bring together the world’s leading proteomic and proteogenomic researchers including those working on cancer research in the company of government, academia and industry leaders. The event will focus on both raising awareness of HUPO and its activities, and advances in proteomics and their impact on human health, as well as the ICPC which currently comprises 11 countries and seeks to encourage more institutions to join this global partnership.

“Every day, every minute matters to patients and we must bring that sense of urgency to our cancer research and care systems.”

Joe Biden

Catalyzed by the efforts of the Cancer Moonshot launched in 2016 by the 47th U.S. Vice President Joseph R. Biden Jr., this year’s HUPO Annual World Congress (HUPO2017) will encourage further collaborations among countries and institutions that represent the great diversity of people and of cancers. Echoing the call of the Cancer Moonshot to accelerate progress against cancer around the world, ICPC (International Cancer Proteogenome Consortium) has currently signed Memorandums of Understanding with 11 countries, encompassing multiple institutions that have pledged to publicly share their proteogenomic data (hosted by the U.S. National Cancer Institute) to accelerate the understanding of common and rare cancers around the world. ICPC teams use an integrated proteogenomic approach, as previously shown by the U.S. National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) to provide more information and insight into cancer’s development and growth, with the aim of leading to better patient care. 

For further information and details, contact:

HUPO2017: Professor Steve Pennington: stephen.pennington@ucd.ie

HUPO: Chelsea Prangnell: chelsea@hupo.org

U.S. National Cancer Institute: ncipressofficers@mail.nih.gov

Dear HUPO colleagues,

HUPO takes knowledge transfer seriously in the current increasingly competitive communication and funding circumstances. The HUPO Marketing Committee is assembling a series of exciting scientific/clinical/technological Success Stories that either proteomics and/or HUPO have delivered.

The taskforce (Mark Baker (chair), Christoph Borchers, Michelle Hill, Pierre Legrain, Charles Pineau and Lennart Martens) asks you to illustrate/describe the Success Story. In addition, the committee will seek comments about impact from eminent researchers and industry alike. These Success Stories will be assembled annually into a constantly growing portfolio, and when each story is complete it will be made available in high-quality print as pdfs, through Facebook, LinkedIn, Twitter, on our integrated HUPO/HPP website and through our HUPO and HPP newsletters.

The committee will accept Success Story suggestions at any time, preferably through the following web-based nomination form: 

http://tiny.cc/HUPO_SuccessStories

Scientists, clinicians and industry are all encouraged to submit.

Please feel free to communicate any proteomics/HUPO breakthrough Success Story.

Thanks.

Best always,
Mark

Mark S. Baker

Past President | Human Proteome Organization 

The neXtProt peptide uniqueness checker maps uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants. The use of this tool is recommended in the latest HPP guidelines as it can be used to define which peptides can be used to validate the existence of human proteins. The tool is described in the recently published Bioinformatics Application Note https://doi.org/10.1093/bioinformatics/btx318.

The 6th newsletter of the Chromosome-centric Human Proteome Project is now available online, read it here. 

In this issue:

• Editorial
• C-HPP Leadership Update
• C-HPP Principal PIC
• A Brief Introduction Of New PIs and Plans
• JPR SI Call For Papers
• Working Group Formation of C-HPP
• Briefings in the 2016 C-HPP Workshops 
• Future C-HPP Workshops

The hPOP (Human Personalized Omics Profiling) project is designed to study the variance of molecular markers across a large number of participants. Recent advances in high throughput technologies allow profiling of thousands of analytes within a single experiment. These measurements could potentially be used to diagnose disease early, monitor treatment progression and stratify patient groups to ensure each individual obtains the treatment best suited to their needs. This personalized approach to medicine would include continuous monitoring of thousands of parameters over a whole lifetime. However, in order to be able to interpret such data, we need to have a better understanding of the underlying natural variation of these molecular parameters in health and disease. Only if we know the natural ranges of individual analytes, the expected responses to perturbations and the long-term trends in their levels, can we draw meaningful conclusions from comprehensive personalized profiling.

In this project, we aim to use a multi-omics approach to study the genome, epigenome, transcriptome, proteome and metabolome of a large number of healthy volunteers. The hPOP project will be launched officially at the 2016 HUPO in Taipei where samples from several hundred people will be collected. The current protocol includes sampling of blood, urine and stool after overnight fasting. Additionally, a detailed questionnaire about food habits, personal health, physical activity and stress levels will be filled out by each participant. All data will be made available to the scientific community under public domain which will allow multiple research groups to use the generated data in their own studies and perform their own analysis of the data.

To find out more or to join the hPOP mailing list, visit the website. 

Proteogenomics, integration of proteomics, genomics, and transcriptomics, is an emerging approach that promises to advance basic, translational and clinical research.  By combining genomic and proteomic information, leading scientists are gaining new insights due to a more complete and unified understanding of complex biological processes.

Advanced bioinformatics approaches are needed to entirely use the complete information spectra acquired in genomics, transcriptomics and proteomics studies.  A DREAM Challenge offers a chance to crowdsource the analysis of numerous rich data sets at once (one of the largest public repositories of proteogenomic sequence data) and thereby compare aspects of various methods to better understand biological features that drive early cancer progression.

To this regard, the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, in partnership with DREAM Challenges, announce the NCI-CPTAC DREAM Proteogenomics Challenge (estimated launch date is mid-June).  The aim of the challenge is to encourage the generation of computational methods for extracting information from the cancer proteome and for linking those data to genomic and transcriptomic information. The goal is to predict proteomic and phosphoproteomic data from multiple other data types.  Method performance will be blindly evaluated using a previously unseen validation dataset generated by CPTAC.

DREAM Challenge will be run in the Google Cloud, and provide a prize award sponsored by the NVIDIA Foundation.  Nature Methods also supports the submission of an overview paper of the Challenge, contingent on a standard evaluation process.

For Registration, click here

Please visit the DREAM website for further details on DREAM challenges, including history, previous challenges and FAQs.

Dear HUPO colleagues,

The HPP is reaching out to clinical scientists or clinicians who are using or consider using proteomics for their research projects. HPP is supporting six (6) clinical scientists with a travel grant to attend the 2017 HUPO World Congress in Dublin, Ireland that will take place from September 17-21, 2017.

Travel grant recipients will receive USD $1,000 to offset travel and hotel costs in addition to complimentary congress registration. The recipients are expected to actively participate in the HUPO congress, particularly in the activities and discussions related to the HPP. Further information on the HUPO 2017 congress and HPP activities in Dublin can be found at http://hupo2017.ie/.

Application deadline: Friday, June 30, 2017

For more information and application instructions visit https://hupo.org/HPP-Clinical-Scientist-Travel-Grants.

Congratulations to the HUPO2016 Taipei PhD abstract competition winners!

Christopher Ashwood (Macquarie University, Australia)

At HUPO, I saw innovative techniques that I had not been exposed to before this conference. I felt inspired by watching a great range of presentations by world-renowned experts in their area of expertise and particularly enjoyed the sessions on glycoproteomics. During breaks between sessions, I was exposed to a huge range of posters from researchers all around the world.

Thanks to the mentoring pre-conference workshop, I learned about the current challenges and expectations in academia. My PhD experience has also been improved by learning about the best current practices in the field of proteomics. Due to this conference, I’ve been able to be up to date on the most recent advances in instrumentation as well as using existing technology to address well-known challenges. The most important point I took away from this conference was the importance of bioinformatics in processing big data sets for more effective biological studies.

During my attendance of HUPO 2016, I felt encouraged that my research area is important to HUPO and thankful for the organising committee for setting up this conference.

Margherita Dell´Aica (ISAS, Germany)

Last year I had the unique experience to attend the HUPO World Congress in Taipei. The program was packed with exciting talks covering cutting edge research, e.g. Technological Advancements, PTMs, Computational Omics and Cancer Research, rendering it the ideal opportunity to promote my own work. The key-note lectures provided deeper (historical) insights and I enjoyed listening to top speakers I only knew from articles.

I am very pleased that I became one of three winners of the HUPO PhD abstract competition. Getting more actively involved into this super-international community and the great experience to promote and defend my work in front of leaders in the fields truly were inspiring and motivating.

The Conference atmosphere was remarkable, such as the kindness of the Taiwanese, the food, the beauty of Taipei’s cosmopolitan streets and the relaxing view of Sun Moon Lake.

Altogether, participating the HUPO 2016 provided me high professional feedback, novel ideas to improve my work, to collaborate with other scientists, and to further pursuit my scientific goals and career. I will definitely participate again in coming years.

Zhiduan Su (University of Sydney, Australia)

It is my great honour to attend 15th HUPO congress in Taipei, which is also an unforgettable experience to me. I also need to thank HUPO 2016 Committee to give me an opportunity to present my study in this congress. My project is about redox proteomics and cysteine oxidations and so far focused on metabolism-disordered cell models. It was really a fantastic and precious occasion that almost all "redox proteomics stuff" could get together and exchange opinions with each other during the congress that might contribute to better understanding of our studies. Also, I was able to meet a few "big guys" and listened to what they were doing recently and what they wanted to do next, which were relevant to the present and future of proteomics progress. Certainly, meetings with old friends during the conference were the memorable moments in my life as well.