Newsletter of the Human Proteome Organization

Current and past HUPOSTs are posted here for your review. Stories, highlights, news, and announcements are gladly accepted for inclusion in the HUPOST. Please submit your information to the HUPO Office at office@hupo.org.

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  • 09 Jan 2020 10:48 AM | Anonymous

    Olga Vitek, Northeastern University, USA

    The May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on April 27 – May 8, 2020 on the campus of Northeastern University in Boston MA, is now accepting applications. The application deadline is January 31, 2020.

    New this year is a "Future developers meeting", a 2-day program that brings together developers (and aspiring developers) of R/Python tools for mass spectrometry and proteomics. We invite you to submit an abstract and present your research at the workshop.

    Participants can select a subset of the following programs:

    * Targeted proteomics with Skyline

    * Proteomics and metabolomics with OpenMS

    * Beginner’s statistics in R

    * Intermediate R and data visualization

    * [NEW THIS YEAR!] Future developers meeting

    * Statistics for quantitative mass spectrometry

    * Scientific writing

    * Capstone – case studies in data-independent acquisition (DIA)

    Instructors are leading experts, who contributed numerous experimental and computational methods and software. The target audiences are both beginners and experienced scientists, with both experimental and computational expertise.

    Tuition fee waivers and travel fellowships will be available for students and postdocs affiliated with academic or nonprofit institutions in the US. Accepted presenters at the Future developers meeting will have a free admission to this part of the program.

    More information is at https://computationalproteomics.khoury.northeastern.edu/

  • 09 Jan 2020 10:26 AM | Anonymous

    C-HPP Executive Committee (EC)

    The C-HPP EC members wish all members of HUPO a Happy and Successful Year in 2020!

    We look forward to the chromosome teams continuing their efforts on identifying more missing proteins and characterizing uPE1 proteins at this juncture of new decade. The following events and publications will highlight our scientific endeavors for exploring new proteins and their functions which you are always welcome to join us.

    February, 2020: New release of neXtProt that will update the status of Missing Proteins, uPE1 protein and other related information for the Human Proteome Project of HUPO.

    May 15-18, 2020: 23rd C-HPP Workshop on the theme of “From chromosome-centric project to the human proteome, which commemorates the 10th Anniversary of the C-HPP Initiative”. This annual C-HPP workshop will be taking place in Saint Petersbourg, Russia and on a cruise ship. The Preliminary Program and registration information will be available soon at the end of January.

    May 31, 2020: Deadline of manuscript submission for JPR Special Issue on the Human Proteome Project (Targeted Publication Date: 1st week of December, 2020)

    August 1, 2020: Publication of C-HPP Newsletter No. 9

    October 18, 2020: 24rd C-HPP Workshop during the 19th HUPO Congress, Stockholm, Sweden.

    October 21-22, 2020: HPP Workshop, Upsala, Sweden

    The C-HPP Wiki

    The C-HPP wiki is continually being updated and we require your input for the individual chromosome teams. Each chromosome group can upload themselves or send their neXt-MP50, neXt-CP50 progress and other update for their chromosome to Peter Horvatovich (see C-HPP Wiki).

    We anticipate that you will join us and contribute to these exciting events and publications throughout this year of new decade.

  • 09 Jan 2020 10:14 AM | Anonymous

    Fernando Corrales, Centro Nacional de Biotecnologia, CSIC, Spain

    The Biology and disease driven Human Proteome Project (B/D-HPP) is one of the international initiatives launched by HUPO to elucidate the molecular basis of human biology and disease progression, to uncover protein drivers of human disease and to promote the development of novel proteomics-based tools to improve the clinical management of patients. Through this activity, the B/D-HPP aims to promote the use of proteomics by the broad scientific community and to translate proteomics findings into medical applications for the benefit of patients.

    The B/D-HPP currently encompasses the efforts of 19 independent initiatives (https://www.hupo.org/B/D-HPP) that focus their activity in specific organs (Brain, EyeOme, Kidney&Urine, Liver, Muscle Skeletal, Plasma), diseases (Cancer, Cardiovascular, Diabetes, Infectious Diseases, Protein Aggregation, Rheumatic and Autoimmune), populations (PediOme) and other topics (Extreme Conditions, Food and Nutrition, Glycoproteomics, Immunopeptidome, Mitochondria, Model Organisms).

    Since 2017 I had the great honor of coordinating the B/D-HPP with the indispensable commitment of the Executive Council integrated by Jenny Van Eyk, Ileana Cristea, Hui Zhang, Paola Roncada, Sanjeeva Shrivastava, Tadashi Yamamoto, Eric Deutsch, Gil Omenn, Mark Baker, Ferdinando Cerciello, Michelle Hill and Vera Ignjatovic). During this time the B/D teams have made outstanding contributions to their respective fields, as reflected by the increasing number of published papers, as well as by the participation in activities from clinical/biomedical societies in their specialized congresses and educational activities. These outstanding achievements have been compiled in annual reports that illustrate the unprecedented capability of proteomics to understand human biology and disease and the significant improvement made in the direction of democratizing the use of proteomics, one of the main goals of the initiative. Besides the activity and strategic discussions, and reports shared with the community, some of the success stories from B/D-HPP teams are communicated each year as part of the main program sessions in the HUPO World Congress.

    January 2020 marks the start of a new period for the B/D-HPP and new challenges are already on the table to ensure the dynamism and enthusiasm of individual teams and the overall initiative under the HPP umbrella.

    First, we should increase our visibility and facilitate the incorporation of scientists to the active teams to consolidate multidisciplinary communities that promote the translation of proteomics technology into clinical applications. This can be achieved by maintenaning a close collaboration with the Early Career Research (ECR) Community. In my opinion, this is a priority that works in two directions, participating in the outstanding ECR initiatives and incorporating the ECRs and their inputs into the B/D-HPP strategy.

    Second, we should potentiate our strengths by enhancing our networking across the HPP initiatives and teams. Apart from the research programs currently active within the HPP initiatives and Pillars, the next B/D-HPP challenge relates to functional annotation of proteins in their biological environments. In this regard, sharing technological resources, data, samples (rare cells and tissues, for instance) and knowhow, appears as a priority for future steps by the B/D- HPP. To this end, the C-HPP, B/D-HPP and the four HPP Pillars must define a common framework to facilitate their crosstalk, as well as the enable interaction with the broad scientific community.

    Starting in January 2020 the B/D-HPP ship will be captained by Ileana Cristea, who has brilliantly coordinated the Infectious Diseases team over the course of the last few years. Moreover, Ileana has been participating at various levels in the HUPO structures and, therefore, has the capacity to integrate a detailed knowledge of HUPO and B/D-HPP strategy, ensuring a smooth transition and outstanding progress in the next two years.

  • 09 Jan 2020 9:57 AM | Anonymous

    HUPO2020 Congress Organizers 

    With much excitement, we are pleased to announce that the Scientific Board is putting together an out of the ordinary program.

    Encompassing the Congress’s theme of ‘Clinical Proteomics for the Benefits of the Patients’, the 19th Human Proteome Organization World Congress will bring together biopharma and biotech drug developments with dedicated sessions within system biology, as well as disease areas such as oncology, cardiovascular diseases, pulmonary diseases, neurodegenerative diseases, and infection/immunology. The official Program at a Glance is now available for viewing on the Congress website.


    We will be launching Registration and Accommodation information in the early new year. For all updates regarding the HUPO 2020 World Congress, please follow the hashtag #HUPO2020 on our social media channels or sign up for our newsletter.

  • 29 Nov 2019 11:02 AM | Anonymous

    Young-Ki Paik, Yonsei Proteome Research Center, Yonsei University, Republic of Korea

    The current HUPO logo was created on July 24, 2001 while Prof. Sam Hanash was serving his first year as HUPO Inaugural President (2001-2004). Sometime in June, Prof. Sam Hanash (Sam) and Prof. Young-Ki Paik (Young-Ki), HUPO Secretary General (2001-2006), discussed the idea of creating a HUPO logo. After this chat, Young-Ki started looking for a reputable and successful branding and naming company in Seoul, Korea. One day, Dr. Sang Yun Cho, one of Young-Ki’s staff members at Yonsei Proteome Research Center (Yonsei University, Seoul, Korea), introduced Prof. Hyewon Sohn, CEO of Crosspoint International Branding and Design Company, located at Hongick University, near YPRC. Her company had had much previous success creating names and logos for major famous companies. Young-Ki met Prof. Sohn and her colleague, Mr. Seoung Woo Hong, and requested that they design the HUPO logo. She asked Mr. Hong, her associate, to do this work, and later he presented three different versions of the HUPO logo as seen in Fig. 1. Because Young-Ki wanted feedback on these three candidate HUPO logos from the proteomics experts, he put them to a vote at KHUPO’s inauguration meeting in Seoul on July 24, 2001. As seen in the image (Fig. 1), the current version received the majority of votes from the attendees at the inaugural KHUPO meeting. Young-Ki immediately sent the current HUPO logo to Sam for his approval. Sam and the HUPO Executive members very much liked it and accepted it as the official HUPO logo.

    After the HUPO logo was created, KHUPO used it to produce the KHUPO logo simply by adding the letter ‘K’ in front of the HUPO logo. Young-Ki and KHUPO thanked both Prof. Sohn and her associate Seoung Woo Hong for their excellent work on the HUPO logo, which they did free of charge. Later on, as a gesture of appreciation to both, Young-Ki presented them with some compensatory gifts on behalf of the KHUPO members. Some years later, Young-Ki also formally offered to donate the logo to HUPO for permanent ownership. Sam and HUPO EC gladly accepted this HUPO logo and authorized it for HUPO administration.

    Note that the 8 blue dots inside the letter “P” each symbolize one letter of the word “proteome”.

    When HPP was launched in 2010 in Sydney HUPO Congress, Young-Ki’s team (Dr. Seul-Ki Jeong) created the current HPP and C-HPP logos by using the “P” (in blue color). The character, ‘P’ now becomes very popular letter for HUPO projects (Fig. 2)


    Figure 1: Shown here are three candidates of HUPO logo which were subjected to voting by KHUPO members in 2001. The current version (middle) received the most popular votes and thus was taken by HUPO.



    Figure 2: Types of Logos of HUPO, HPP and C-HPP 

  • 29 Nov 2019 10:43 AM | Anonymous

     

    Chris Overall, University of British Columbia, Canada

    Publishing in the first week of December, the seventh annual special issue of the Journal of Proteome Research dedicated to the HPP has 20 major contributions from the two HPP initiatives, the Chromosome-centric HPP (C-HPP) and the Biology/Disease (B/D-HPP) HPP, and four Resource Pillars in Mass Spectrometry, Antibody-Profiling, Knowledgebase, and Pathology.

    Based on the January 2019 updates of curation and annotation of the human proteome by neXtProt (https://www.nextprot.org/) from the standardized reanalysis of mass spectrometry datasets by PeptideAtlas (http://www.peptideatlas.org/), which form the baseline for the 2019 papers in this special issue, Omenn et al (2019) report that highly credible evidence supports Protein Evidence Level 1 (PE1) for 17,694 protein-coding genes, 89.3% of the total of 19,823 predicted human protein-coding genes. In this annual metrics of the human proteome paper, these numbers represent a net increase of 224 PE1 proteins, due to promotion of 213 PE2,3,4 entries to PE1, but with a net decrease of only 57 missing proteins (MPs) due to 60 PE1 demotions and 116 new PE2,3,4 entries.

    Many strategies have been deployed to detect the neXtProt missing proteins: analysis of more diverse specimens including the first large scale proteome analysis of young adult human bone, use of much more sensitive mass spectrometry instruments, enrichment of low-abundance proteins, solubilization of membrane proteins, and the use of multiple proteases. This year’s Special Issue continues that endeavor.

    Shteynberg et al 2019 have developed PTMProphet, open-source software for facilitating the calculation of confidence metrics for the precise localization of PTMs. Since its associated algorithms were integrated into the Trans-Proteomic Pipeline platform, this tool has been used to assess PTMs with different numbers of modifications and modified sites using the information content to yield correct localization for 1164 PTMs at less than a 1% false localization rate.

    These are but a few highlights of the important compilation of papers highlighting the progress of the HPP.

    Omenn, G. S.; Lane, L.; Overall, C. M.; Corrales, F. J.; Schwenk, J. M. et al., Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. J Proteome Res 2019.

    Deutsch, E. W.; Lane, L.; Overall, C. M.; Bandeira, N.; Baker, M. S. et al. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. J Proteome Res 2019.

    Shteynberg, D. D.; Deutsch, E. W.; Campbell, D. S.; Hoopmann, M. R.; Kusebauch, U. et al., PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. J Proteome Res 2019.

    The new HPP Data Guidelines v 3.0
    A key paper that needs close attention in the hunt for missing proteins is from Deutsch and colleagues 2019 who now report the HPP Guidelines v3.0, based on wide consultations with the HPP community over the past year. Key features of v3.0 are a reorganized main checklist, addition of guidelines for data-independent acquisition workflows and for use of the Universal Spectrum Identifier developed by the HUPO Proteomics Standards Initiative (PSI), an updated HPP pipeline for standardized reanalysis of MS datasets generated throughout the community, and a plan for incorporating MassIVE-KB into the HPP pipeline. This timely update maintains the high quality of MS-based data, which is essential for creating a credible chromosome-centric protein parts list for the entire human proteome.

    The C-HPP Wiki
    The C-HPP wiki is continually being updated and we require your input for the individual chromosome teams. Each chromosome group can upload themselves or send their neXt-MP50, neXt-CP50 progress and other updates for their chromosome to Peter Horvatovich (see C-HPP Wiki).

    Chris Overall (chair), Young-Ki Paik (co-chair), Lydie Lane (co-chair), Gilberto B. Domont (MAL), Fernando Corrales (MAL), Pengyuan Yang (MAL) and Peter Horvatovich (secretary general).

  • 29 Nov 2019 9:43 AM | Anonymous

    Tadashi Yamamoto, Former chair and current co-chair Niigata University, JAPAN.
    John M Arthur, Current chair, University of Arkansas for Medical Sciences ,USA.

    The first-generation HKUPP was established as the 11th initiative in the World HUPO Congress by gathering about 40 researchers from around the world in 2007 with the following missions:

    • To facilitate proteome analysis and foster proteomics researchers in nephrology.
    • To understand kidney functions and pathophysiology of human kidney diseases
    • To provide kidney and urine proteome databases for discovery of biomarkers and drug targets.

    In the next 10 years (2007-2017), the HKUPP members had several meetings during the World HUPO Congresses and the American Society of Nephrology meetings to exchange the data and information on proteomic analysis of kidney tissue and urine samples. As a contribution to urine proteomics researchers, we proposed a guide or recommendation of how to collect and store urine samples suitable for proteome analysis (Sci Transl Med. 2010 Aug 25;2(46):46ps42. doi: 10.1126/scitranslmed.3001249.). Proteome data of urine samples and kidney tissues from normal healthy volunteers were also collected and made available in the HKUPP website (www.hkupp.org). Comparison of the proteomes of these tissues and plasma/urine provided tissue(-compartment)-unique proteins, as well as urinary proteins uniquely derived from these tissues. Those proteins were therefore expected to be proteins that might play specific roles in these tissues, or proteins which might indicate pathological events.

    In 2017 the new chair of HKUPP, Prof. John M Arthur started to re-organize the HKUPP team to promote the second-generation project to apply the current advanced techniques and instruments to clinical samples. Samples such as kidney biopsy specimens and patient urine will be useful to understand pathology and to establish urine biomarkers for clinical assessment (Fig.1).

    In 2019 we had a meeting in Washington DC during the American Society of Nephrology Kidney Week 2019 to discuss the plans related to the 2nd generation HKUPP and the possibility for collaborative grant application such as RC2 of NIH to facilitate the international activities of the HKUPP initiative.

    Figure. 1 Promotion of HKUPP activities from the 1st generation to the 2nd generation: From basic science to clinical contributions


  • 28 Nov 2019 3:31 PM | Anonymous


    Human 10th birthdays mark a very special tradition – from a learning-packed early childhood to wonderfully exhilarating teenage years. Similarly, at the 19th Human Proteome Organization World Congress in Stockholm, the Human Proteome Project (HPP) celebrates this milestone decadal birthday by releasing the first community-endorsed blueprint draft of the human proteome.

    It was only two decades ago that a company (Celera Genomics) and public rivalry under the Human Genome Project assembled the draft human genome. This contained far fewer protein-coding genes than was anticipated and was jam-packed with gaps and ambiguities. Recent analysis suggests that the human genome only codes for approximately 20,000 proteins. Arms with the draft genome, the first challenge was to assemble a parts-list blueprint for the human proteome. This initial phase involved an unparalleled collaborative enterprise, this time involving scientists from over 100 countries with various skill sets, freely uploading and then communally analyzing their data. This now culminates in a high-precision human proteome knowledge base.

    Some sought to find the elusive missing proteins which dodge discovery, whilst others sought to appreciate how human proteome worked or how it could be harnessed to better diagnose and treat cancer, Alzheimer’s, heart attacks, diabetes, and other diseases.

    Join us in Stockholm, Sweden from October 18 – 22, 2020 to celebrate the launch of the collaborative Human Proteome Project blueprint. Read more.

  • 01 Nov 2019 8:53 AM | Anonymous

    Chris Overall, University of British Columbia, Canada

    The 23rd C-HPP workshop will be held aboard the very comfortable river-class cruise ship traveling from Saint Petersburg to Valaam Island and back to Saint Petersburg from Friday May 15 (18:00) to Monday May 18 (09:00), 2020. The focus on of the workshop will be “From chromosome-centric project to the human proteome” and will also nucleate celebrations of the 10th anniversary of the C-HPP Initiative. The workshop is organized by Prof. Alexander Archakov, also celebrating in 2020 his 80th birthday and the and 75th Anniversary of the Institute of Biomedical Chemistry (Moscow, Russia). Thus, many Russian Colleagues in Proteomics and Bioinformatics will also be in attendance making for a rich program.

    The Workshop aims to cover the following scientific topics:

    • Status update from Chromosome, neXt-MP50 and neXt-CP50 teams
    • Bioinformatics Tools Development—from C-HPP to the human proteome
    • Transcriptoproteomics—the way from Genome to Proteome
    • Proteomics Technology Innovations
    • Proteomics and other OMICs—Impact on Medicine
    • Missing proteins in rare tissues and diseases (with B/D-HPP)

    Registration will open soon and we are expecting that support from the Russian Government will be announced late in December, at which time we can release the cost. All information regarding the workshop will be available at the C-HPP Wiki.

    The HUPO C-HPP Chronicle
    The Chronicle of the Chromosome-Centric Human Proteome (C-HPP) project showing the most important milestones of the C-HPP such as building up of the chromosome teams, the C-HPP and then the HPP special issues in Journal of Proteome Research, C-HPP workshops and special events, and key publications is available at C-HPP Wiki.

  • 31 Oct 2019 4:29 PM | Anonymous

    Early Career Research (ECR) Committee

    The HUPO Early Career Researcher (ECR) Initiative is proud to announce that Dr. Justyna Fert-Bober has been nominated as the ECR representative on the HUPO Executive Committee. Dr. Fert-Bober is a co-founder of the HUPO ECR Initiative, a trailblazer and leader in ECR involvement in the proteomics community and a strong advocate of highlighting early career researcher talents. Among other things, she is a co-organizer of the HUPO ECR Manuscript Competition and of the HUPO World Congress Trainee Workshop (Biosketch below).

    This new ECR position on the HUPO Executive Committee was approved by the HUPO Council and announced at the most recent HUPO General Assembly. The HUPO ECR Initiative would like to thank the HUPO Council for their continuous support of proteomics early career researchers and for giving them a voice on the HUPO Executive Committee.


    Dr. Justyna Fert-Bober. Research Scientist I
    Cedars-Sinai Heart Institute 

    Dr. Justyna Fert-Bober’s Biosketch

    Dr. Fert-Bober is a Research Scientist I at the Cedars-Sinai Heart Institute. She obtained her B.Sc. and M.Sc. degrees in Biochemistry and Molecular Biology from the University of Wroclaw and her Ph.D. in Clinical Chemistry from Medical University, Wroclaw. She then performed her postdoctoral research at The Johns Hopkins University School of Medicine. Dr. Fert-Bober is a pioneer in the understanding of arginine deiminases and protein citrullination’s contribution to molecular and cellular mechanisms of heart failure in the general population and in the immunopathogenesis of heart disease in rheumatoid arthritis patients. She has published over 17 papers on these topics. Dr. Fert-Bober’s overarching research goal is to identify panels of biomarkers and drug targets that can be used in the development of novel diagnostic and therapeutic approaches to not only treat patients for a limited time, but to change underline disease processes. In addition, Dr. Fert-Bober is dedicated to raising the profiles of early career researchers. She is the co-founder of the HUPO Early Career Researcher Initiative, which main objectives are to provide training opportunities to early career researchers and to showcase their work and talent on the international stage.

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