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A real success story of international collaboration through HUPO was the launch of the International Cancer Proteogenome Consortium (ICPC) during the 2016 HUPO Congress in Taipei.
Story by Michelle Hill, B/D-HPP Newsletter Editor
Some of the ICPC representatives at HUPO 2016 in Taipei. From left: Daehee Hwang (South Korea), Ruedi Aebersold (Switzerland), Christoph Borchers (Canada), Henry Rodriguez (USA), Albert Sickmann (Germany), Mark Baker (Australia), Chia-Jung Yu, Yu-Ju Chen, Min Daw Tsai, Chen-Yang Shen (Taiwan).
This exciting development was grounded on ongoing collaboration between the Cancer Initiative of the B/D-HPP and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of The United States National Cancer Institute (NCI), and nurtured through years of work at HUPO Congresses. Following the first announcement in Australia in July 2016, an additional 7 countries now joins the initiative to form the International Cancer Proteogenome Consortium (ICPC). This is a real success story of international collaboration catalyzed by HUPO. Two of the leaders tell of the story.
Read the full story in the B/D-HPP Newsletter | Issue 1, 2017
The Human Proteome Organization presents awards annually at the World Congress. The HUPO 2017 World Congress is in Dublin from September 17-21. Award recipients will present a brief talk during the Congress award ceremony. These distinguished awards recognize the outstanding efforts of individuals (or groups) advancing the field of proteomics. Nominations are done through an online submission form and no supporting documents or attachments are required.
You are invited to nominate award candidates!
Nomination Deadline: April 17, 2017
HUPO is now accepting nominations for the following awards:
Distinguished Achievement in Proteomic Sciences Award ($3000, sponsored by Journal of Proteome Research - ACS Publications) recognizes a scientist for distinguished scientific achievements in the field of proteomic science.
Discovery in Proteomic Sciences Award ($3000, sponsored by Journal of Proteomics - Elsevier BV) recognizes a scientist for a single discovery in the field of proteomics.
Science and Technology Award ($3000, sponsored by the HUPO Industrial Advisory Board) recognizes an individual, or team (of up to three people) in private industry who played a key role in commercialization of a proteomics technology, product or procedure. The emphasis for the award is on making the technology, product or procedure widely available, which is different from the basic scientific invention.
Clinical and Translational Proteomics Award ($3000, sponsored by Clinical Proteomics - BioMedCentral) recognizes a scientist for distinguished scientific achievements in the field of clinical and translational proteomics.
Distinguished Service Award ($3000, sponsored by HUPO) recognizes an exemplary member of the proteomic research community whose dedicated service has made indispensable contributions to the organization and mission of HUPO.
Media Release from Macquarie University - 23 January 2017
Much remains to be understood about how proteins in the human body works in unison; however a newly developed resource is giving scientists a more complete picture of how the proteome makes us uniquely human. MissingProteinPedia, a database developed by a collaborative research group lead by scientists at Macquarie University, could not only help researchers learn more about the location and use – termed ‘expression’ – of specific proteins in the body but also how they interact to make us human. It will also help to pin down those proteins which are still ‘in the shadows’, with implications for several diseases.
Dr Shoba Ranganathan and Dr Mark S Baker
Photographer credit: Paul Wright
“While we know a lot about individual proteins, the larger picture of how these proteins work together to make an individual person is a difficult concept to explore. Although we are developing new technologies to test when, where, why and how proteins are expressed, we still need some way of tying all the biological information together so that we get a clearer picture of how proteins work together to turn us into an individual human being,” explained Professor Mark Baker, lead author of the missing protein study.
“Our team developed MissingProteinPedia to gather all the scattered and incomplete information about what the Human Proteome Project calls missing proteins. This includes the 2,949 proteins that, despite rigorous testing, are still ‘in the shadows’ and haven’t yet been proven to exist,” he added.
The tool accelerates the discovery of many missing proteins, particularly those in elusive protein families, with potentially vast consequences for human disease.
“In order to understand how a disease progresses we need a detailed picture of how all proteins work in a healthy individual, so that we can understand what triggers the development of diseases,” explained senior author Professor Shoba Ranganathan.
“MissingProteinPedia has uncovered substantial evidence for many hard-to-detect proteins for which small amounts of information have taken years to gather. The very fact that we have come so far in such a short time bodes well for our understanding of complex human diseases such as cancer,” she added.
The researchers will make the database a community-driven, citizen-science project where everyone can help in the discovery of human missing proteins and their role in health and disease.
Media Contact: Dr Megan Wright | T: +61 (2) 9850 1055 | E: megan.wright(at)mq.edu.au | A copy of this release will be available online at www.mq.edu.au/newsroom
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:
Scientists, clinicians and industry are all encouraged to submit.
Please feel free to communicate any proteomics/HUPO breakthrough Success Story.
Mark S. Baker
Past President | Human Proteome Organization
The Bioinformatics Hub is a place where bioinformaticians gather together with three aims: (i) to provide their advice, knowledge, and support to anyone with a relevant question; (ii) to discuss current issues and challenges in proteomics informatics with the entire community; and (iii) to work on interesting, synergistic projects and to freely exchange tools, algorithms and know-how with each other, across all labs, seniorities and levels of experience.
The Bioinformatics Hub at the HUPO 2016 World Congress in Taipei was highly successful in bringing together many researchers interested in computational proteomics and bioinformatics to discuss topics important in the field. The hub was open daily from 8:30 – 5:30 during the congress, and the on-line program dynamically updated hourly with ongoing activities. Some of the more prominent topics addressed included discussions over the HPP Data Interpretation Guidelines v2.1, The HPP 50 Missing Protein Challenge, the proposed JPR Bioinformatics/Computational Resources Special Issue, use of preprint servers for computational proteomics manuscripts, MissingProteinPedia, privacy implications of proteomics data, OmicsDI, glycoproteomics informatics, quality control formats, and proteogenomics data file formats. Work on these topics will proceed based on these discussions, and we look forward to another exciting Bioinformatics Hub at next year's HUPO World Congress. See the Bioinformatics Hub web site for more information: https://github.com/CompMS/Overview/wiki/HUPO-2016
-Written by Eric Deutsch, Yves Vandenbrouck and Lennart Martens
HUPO Chromosome-Centric Human Proteome Project (C-HPP) has recently published its 4th Special Issue of the Journal of Proteome Research (http://pubs.acs.org/toc/jprobs/15/11) which carries a total of 18 papers. This special issue highlights the progress on the C-HPP and its related projects in many aspects such as HPP Mass Spectrometry Data Interpretation Guidelines, 2016 HPP Metrics, Discovery of 267 Missing Proteins (currently 2930 proteins) and other biological aspects of newly identified proteins encoded by human chromosomes.
“We are delighted to be part of this CPTAC initiative and to be able to contribute to this important project. The University of Victoria-Genome BC Proteomics Centre will continue to develop MRM assays according to the CPTAC guidelines and upload them to the CPTAC portal. In addition, we intend to further develop these CPTAC MRM assays as validated kits to facilitate their use by the broader scientific community.” – Dr. Christoph Borchers, Ph.D., Director of the University of Victoria Genome BC Proteomics Centre, Canada
“We are excited to align forces with Christoph to provide open source, highly characterized, targeted MS assays to the community. The ability to reliably quantify proteins is a critical next step towards making the genome actionable and improving our understanding, diagnosis, and treatment of diseases. ” – Dr. Amanda Paulovich, Member of the Fred Hutchinson Cancer Research Center and co-Chair of the CPTAC Assay Development Working Group
“This generous contribution and future commitment by Christoph at the University of Victoria Genome British Columbia Proteomics Centre to deposit well-characterized, targeted MS assays into CPTAC’s Community Assay Portal which employ an experimental/analytical fit-for-purpose approach, will accelerate the evolution from genomics to proteomics.” – Dr. Henry Rodriguez, Director of the Office of Cancer Clinical Proteomics Research at the National Cancer Institute, National Institutes of Health
The below press release was sent by the NCI Office of Cancer Clinical Proteomics Research on August 29, 2016.
University of Victoria Genome British Columbia Proteomics Centre, a leader in proteomic technology development, has partnered with the U.S. National Cancer Institute (NCI) to make targeted proteomic assays accessible to the community through NCI’s CPTAC Assay Portal (https://assays.cancer.gov).
A key aspect of the Assay Portal is to provide space where national and international proteomics researchers from across the globe can upload and share their quantitative assays with standard operating procedures and guidelines. To meet this goal, NCI is continuing to improve the assay upload process to have an independent process for public/non-CPTAC teams to upload their assays in a seamless fashion and will provide update on this effort to the community as it comes available.
Targeted proteomic assays eliminate issues that are commonly observed using conventional protein detection systems (e.g. Western blotting), which are semi-quantitative at best, not readily multiplexed, and often non-specific. Until recently, non-standardized information for hundreds of targeted mass spectrometry-based assays was distributed across published journal articles. The CPTAC assay portal serves as a centralized public repository of highly characterized targeted MS assays, including standard operating protocols, reagents, and assay characterization data.
Dr. Christoph Borchers, Ph.D., Director of the University of Victoria Genome BC Proteomics Centre, Canada, has volunteered to be the first non-CPTAC researcher to upload targeted mass spectrometry-based assays to the portal. These multiple reaction monitoring (MRM-MS)-based assays fully adhere to the standards and guidelines developed by CPTAC and meet the minimum characterization requirements for entry to the portal, including development of multipoint response curve and repeatability assessment. In the portal landing page, which is designed to be relevant to biologists, researchers will be able to search for the Proteomics Centre assays by querying using the “non-CPTAC” term. Dr. Borchers has contributed 107 MRM assays to the portal in this initial phase, and is working on completing up to 2,000 assays that will be ultimately imported to the CPTAC Assay Portal.
“We are delighted to be working with the CPTAC on this important project,” says Dr. Borchers. “Standardization of protein quantitation is essential if mass spectrometry-based proteomics is going to be used for clinical assays. To assist in cancer-related research, we are planning to greatly extend the range of our MRM based assays in CPTAC to include assays for mouse proteins. The mouse is the preferred animal model for studying cancer, and will become even more important through the new CRISPR/Cas9 technology, which greatly facilitates the research of genetic mutations of cancer-related proteins in mice at a low cost.”
Dr. Amanda Paulovich, a Member of the Fred Hutchinson Cancer Research Center and co-Chair of the CPTAC Assay Development Working Group, notes that, “We are excited to take this important first step in opening up the Assay Portal for contributions from the entire community, bringing us one step closer to the goal of standardizing quantification of all proteins across the community to improve analytical rigor and reproducibility in protein-based research.”
To empower researchers and democratize protein measurements, NCI launched the proteomics Assay Portal in 2014. This community web-based repository for well-characterized quantitative proteomic assays which was highlighted in a landmark paper in Nature Methods currently consists of greater than 900 targeted assays and serves as a public resource of methodologies and data related to cancer associated targets. By incorporating guidelines for assay characterization, the CPTAC Assay Portal takes a leap forward in enabling researchers to assess the performance of each assay as well as downloading all the data and information for implementing the assays. The ultimate goal is to standardize protein quantification and harmonize results across laboratories, improving our ability to validate molecular signatures and the reproducibility of preclinical research, as well as facilitating the regulatory approval of new drugs and diagnostics.
The Assay Portal also represents the application of “best practices” for targeted mass spectrometry developed during a two day-workshop held at the National Institutes of Health and published in 2014 in the journal of Molecular and Cellular Proteomics. In this workshop CPTAC, with input from the outside community that included the U.S. Food and Drug Administration and American Association for Clinical Chemistry, established a framework for MRM assay ‘fit-for purpose’ validation by defining three tiers of assays distinguished by their performance and extent of analytical characterization. Assays presented on the CPTAC portal predominantly represent ‘Tier 2’ assays, as described in the workshop report.
THE POWER OF RESEARCH COLLABORATION
About the University of Victoria Genome British Columbia Proteomics Centre
The University of Victoria Genome BC Proteomics Centre is a state-of-the-art proteomics research facility located at the University of Victoria’s Vancouver Island Technology Park in Victoria, British Columbia, Canada. Supported by Genome Canada, Genome BC and the University of Victoria, the Centre is the best-equipped proteomics research facility in Canada, with $10 million worth of specialized equipment including 16 mass spectrometers. The Centre is a not-for-profit facility that operates on a cost recovery model. It is the longest operating proteomics core facility in Canada, having been in operation since 1982, and serves clients in academia, industry and government on a fee-for-service and collaborative basis.
About National Cancer Institute’s CPTAC
The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis technologies (proteogenomics) to different cancer types. CPTAC is composed of expertise in proteomics, genomics, cancer biology, oncology and clinical chemistry, while creating open community resources that are widely used by the cancer community. For further information about CPTAC, go to http://proteomics.cancer.gov.
The 2016 HUPO Council Election results were announced at the General Assembly of Members on September 19, 2016 in Taipei during HUPO 2016. Council terms are three years and will extend from January 2017 to December 2019. We are pleased to congratulate the following future HUPO councilors.
Yasushi Ishihama (Japan)
Terence Poon (Macau)
Anthony Purcell (Australia)
Bernd Wollscheid (Switzerland)
Martin Larsen (Denmark)
Emma Lundberg (Sweden)
Ileana Cristea (USA)
Benjamin Garcia (USA)
Aleksandra Nita-Lazar (USA)
Susan Weintraub (USA)
Diversity Representatives Appointed by Council and Confirmed by Electorate
Sanjeeva Srivastava (India)
Jong Shin Yoo (South Korea)
Ruth Birner-Grünberger (Austria)
Andrea Urbani (Italy)
Gilberto Domont (Brazil)
Four future HUPO Executive Committee positions (for 2-year terms, starting January 2017) were elected during the HUPO Council Meeting on Sunday, September 18.
We are pleased to announce the following future HUPO Executive Committee members.
HUPO Secretary General – Emma Lundberg, Sweden
HUPO Treasurer – Peter Hoffmann, Australia
HUPO Member-at-Large – Lennart Martens, Belgium
HUPO Member-at-Large – Christopher Overall, Canada
Welcome to the first BD-HPP newsletter!
Read the Newsletter Online
This communication is design to inform and encourage collaborative efforts within the HUPO community, within B/D-HPP initiatives as well as across B/D-HPP and C-HPP. In each issue, we aim to highlight the activities and achievements of two B/D-HPP initiatives, and celebrate a success story. The newsletter editor is Michelle Hill, a new HUPO council member from Brisbane, Australia.
The Most Trusted Journal in the International Field of Proteomics
Copyright 2016 - HUPO