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  • 06 Dec 2017 2:16 PM | Anonymous

    Deadline January 14, 2018: Institut Pasteur has launched an international call for junior candidates wishing to establish new independent research groups in the cutting edge interdisciplinary environment of its campus in Paris, France. This year the call will be focused on the topics associated with the INstitut Convergence entitled “Emergence of Pathologies Through Individuals and populatiONs” (INCEPTION program). Read on here


  • 22 Nov 2017 3:34 PM | Anonymous

    Mark HUPO 2018 in Orlando, Florida on your calendar now! Congress dates are September 30 - October 3, 2018. We are pleased to announce there will be an HPP Post-Congress Day on October 4, 2018. Attendees may also look forward to a complete roster of pre-congress activities (workshops and short courses) on Sunday, September 30 before the official congress opening on Sunday evening.

    All congress sessions and special hotel guest room block will be at Loews Royal Pacific located on the grounds of Universal Studios. The congress hotel guest room rate of $189 per night will be available three days pre- and post-congress (based on availability) should you wish to plan some “fun time” at the Universal Studios parks (includes the Harry Potter attraction).

    Visit www.HUPO2018.org on January 15, 2018 for the following:

    • Opening of guest room reservations Loews Royal Pacific
    • Opening of Congress early registration
    • Opening of abstract submission
    • Early deadline for exhibitor and sponsor orders (prices increase after January 15)

    You might have noticed our promotion at HUPO 2017 in Dublin where we invited “Wizards in Training” to take a photo dressed a la Harry Potter. We look forward to seeing these wizards (and a few more) in Orlando next September.


  • 20 Nov 2017 3:04 PM | Anonymous

    A new initiative at HUPO2017 was a round table discussion with clinical scientist travel grant winners, the B/D-HPP executives, selected previous clinical scientist travel grant winners, and HUPO2018 organiser Ileana Cristea. The goal of the round table discussion is to gain insight on the challenging facing clinical scientists in proteomics research, and feedback how HUPO could facilitate their clinical proteomics research. In addition, it was hoped that each of the travel grant winners could work closely within one or more B/D-HPP initiatives.

    The five award winners hail from across the globe, with broad specialities.

    Dr Mariette Labots is a medical oncologist at the VU University Medical Centre, Amsterdam, The Netherlands. She is currently pursuing PhD in the OncoProteomics Laboratory led by Dr Connie Jimenez. Dr Labots has worked on phosphoproteomics of cancer tissues in response to targeted therapies.

    Dr J Robert O’Neill is a clinical lecturer and honorary specialty registrat in upper gastrointestinal surgery, University of Edinburgh, UK. After completing his PhD in 2014, which involved the use of proteomics to explore therapeutic target discovery, Dr O’Neill is currently building a program in esophageal cancer research in Edinburgh.

    Dr Emma Nimeus is a breast cancer surgeon at Skane’s University Hospital and principal investigator for the Breast Cancer Proteogenomics Group at Lund University in Sweden, in the next-door buildilng. Dr Nimeus has established an interdisciplinary and international collaboration to enable proteogenomics research using clinical samples procured from her clinical practice.

    Professor Richard D. Semba is an ophthalmologist from Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. He is one of the leaders of B/D-HPP EyeOME initiative which began in 2012. Prof Semba’s research aims to understand three important blinding eye diseases: age-related macular degeneration, chronic angle closure glaucoma, and idiopathic macular holes.

    Dr Krishna R Murthy is a vitreo-retinal surgeon and the medical director of Vittala International Institute of Ophthalmology, Bangalore, India. He recently defended his PhD from Amrita Vishwa Vidyapeetham. Dr Murthy’s areas of clinical interest include diabetic retinopathy, Retinopathy of prematurity, HIV related eye diseases and proteomics of the ocular structures.

    The round table began with self-introductions of research areas, how proteomics technologies are accessed, and any challenges currently facing the travel award winners. In-depth discussions between the participants explored diverse topics including the need for proteomic (and lipidomic) research, challenges to obtain access to advanced mass spectrometry technologies and to keep abreast of the fast pace of technology change.

    Finally, B/D-HPP executives and HUPO2018 organisers solicited and received feedback on how the HUPO World Congress program could be modified to further facilitate clinical proteomics research and collaboration. Look out for new ideas and formats at HUPO2018!


    From left to right: Hui Zhang (Cancer HPP co-chair), Mariette Labots (grant winner), Ferdinando Cerciello (past grant winner, B/D-HPP ECR rep), Robert O’Neill (grant winner), Emma Nimeus (grant winner), Jenny Van Eyk (B/D-HPP chair and executive committee member), Richard Semba (grant winner), David Herrington (past grant winner), Murthy Krishna (grant winner), Eric Deutsche (B/D-HPP executive committee member). Not pictured: Gil Omenn (B/D-HPP ex-officio), Fernando Corrales (B/D-HPP co-chair), Ileana Cristea (HUPO2018 organiser), Michelle Hill (B/D-HPP news article editor).

  • 23 Oct 2017 11:13 AM | Anonymous

    Protein glycosylation is a common and diverse modification crucial to the understanding of protein function in just about every biological system. Advances in mass spectrometry now allow hundreds and even thousands of unique intact glycopeptides to be identified from a single LC-MS/MS-based glycoproteomics experiment [1]. However, confident identification of intact glycopeptides is still challenging and correct spectral annotation remain heavily dependent on laborious manual expert interpretation of fragment mass spectra. Glycoproteomics is experiencing increasing attention these years not least within the HUPO community as demonstrated with a dedicated glycoproteomics sessions at HUPO2016. However, the described technical limitations are inhibiting new scientists from entering this exciting area of proteomics. Thus, there is a clear need for tools for accurate and confident automated glycopeptide identification.

    The past decade has seen promising developments of a range of MS-based software for intact glycopeptide identification [2]. To enable community evaluation of these developing tools, the new chair of the HGI, Prof Nicki Packer, Macquarie University, Sydney launched a new HGI study at HUPO2017. For this purpose, two large data files containing high resolution tandem mass spectral data of intact glycopeptides from human serum have been generated for this purpose by ThermoFisher. Combinations of dissociation modes (HCD, EThcD, ETciD and CID) were used to obtain the spectra. An expert panel will curate/analyse the data to create a consensus glycopeptide library, for comparison against the list of identifications being reported by participants in the study.

    We are calling for participants (of academic and/or industrial origin) that are either developers of glycoproteomics software and/or expert users (researchers) in glycoproteomics, to identify and report on the characterization of the intact serum glycopeptides using either their own software (developers) or by using one or more tools which they routinely use in their glycoproteomics research including manual interpretation (expert users). Participants are asked to report how they interpreted the data. We plan to send out the intact glycopeptide MS/MS data this year in order to present the preliminary results of the comparative study at the next HUPO in 2018, with a planned publication of the final results and conclusions to follow. Please contact nicki.packer@mq.edu.au if you would like to be part of this study.

    HGI Committee members:

    Prof Nicki Packer (Macquarie University and Griffith University, Australia) (Chair)

    Dr Morten Thaysen-Andersen, Macquarie University, Australia (Deputy Chair)

    A/Prof Daniel Kolarich, Griffith University, Australia (Deputy Chair)

    Dr Stuart Haslam, Imperial College, UK

    Prof Kai-Hooi Khoo, Academia Sinica, Taiwan

    Prof Goran Larson, Gothenburg University, Sweden

    Prof Katalin Medzihradszky, UCSF, USA

    Prof Giuseppe Palmisano, University of Sao Paulo, Brazil

    Prof Jong Shin Yoo, Korea Basic Science Institute, Korea

    Prof Joe Zaia, Boston University, USA

    References:

    [1] Thaysen-Andersen M, Packer NH, Schulz BL. Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease. Mol Cell Proteomics. 2016. 15(6):1773.

    [2] Hu H, Khatri K, Klein J, Leymarie N, Zaia J. A review of methods for interpretation of glycopeptide tandem mass spectral data. Glycoconj J. 2016. 33(3):285.


    Design of the new HGI study to compare the performance of current glycoproteomics software for N- and O-glycopeptide identification from high resolution MS/MS spectral data of a complex mixture of serum proteins.

  • 23 Oct 2017 10:54 AM | Anonymous

    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


  • 17 Sep 2017 1:21 PM | Anonymous

    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.



  • 06 Sep 2017 12:10 PM | Anonymous


    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

  • 20 Jun 2017 11:00 AM | Anonymous member (Administrator)

    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 

  • 29 May 2017 2:29 PM | Anonymous member (Administrator)
    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.
  • 17 May 2017 10:01 AM | Anonymous

    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
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