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  • 31 Jan 2024 9:28 AM | Anonymous member (Administrator)

    Date: Wednesday February 28, 2024
    Time: 4pm GMT (5pm CET)

    Are you a Ph.D. student, postdoc, or early career researcher looking to get recognised for your work? Join the next HUPO Early Career Researcher online panel discussion, "Getting recognised for your work", at 4pm GMT (5pm CET) on Wednesday February 28.

    The panel will feature Dr. Laurent Gatto (Associate Professor of Bioinformatics, UCLouvain), Dr. Stacy Malaker (Assistant Professor of Chemistry, Yale University), and Dr. Juan Antonio Vizcaino (Scientist and Team Leader, Proteomics, European Molecular Biology Laboratory).

    This will be the perfect opportunity to ask any questions that you may have about getting recognised for your work and putting yourself in a favourable position for your future career.

    REGISTER HERE

  • 31 Jan 2024 8:51 AM | Anonymous member (Administrator)


    The C-HPP is holding a workshop Madrid, Spain, at the National Center for Biotechnology, CSIC, Campus of the University Autónoma of Madrid, Darwin, 3, Spain.

    A workshop hotel is being organized where registrants can book and cover their own accommodation. The hotel will be near the train station for a short 15-minute ride to the University Autónoma.

    Registration and most meals and coffee are free and we invite members of the C-HPP, B/D-HPP, and HPP to register as soon as possible to help with planning.

    AGENDA

    The main foci for the Workshop are (i) short business meeting for reports and C-HPP Chromosome team updates.

    Preliminary Program

    Wednesday April 24
    13:00-14:00 Welcome Lunch
    14:00-17:00 Discussion on guidelines for assigning protein function for the Grand Challenge, and incorporating SWATH/DIA data into the HPP. With the loss of support of neXtprot, also to be discussed will be a new repository for HPP progress on completing the Human Proteome Project and where the data will reside for functional annotation of the Human Proteome.

    Thursday April 25
    09:00-13:00 Session One Welcome, the C-HPP Mission, contributing to the HUPO Grand Challenge.
    12:30-13:00 Invited speaker (TBA)
    13:00-14:00 Lunch
    14:00-18:00 Session Two
    14:00-15:30 Three invited speakers (TBA)
    15:30-16:00 Coffee
    16:00-18:00 Open Discussion on Mission of the C-HPP
    19:00 Tapas Dinner in Madrid Center

    Friday April 26
    09:00-13:00 Session Three
    09:00-10:00 Two invited speakers (TBA)
    10:00-10:30 Coffee
    10:30-13:00 Discussion on the Grand Project
    13:00 Campus Restaurant lunch and departure

    REGISTER HERE

  • 31 Jan 2024 8:47 AM | Anonymous member (Administrator)

    The hallmark update paper each year is the HPP Metrics publication, is now online, lead by Dr Gil Omenn and the leaders of neXTprot, the Peptide Atlas, the HPP, C-HPP and B/D-HPP:

    The 2023 Report on the Human Proteome from the HUPO Proteome Project”, by Gilbert S. Omenn,* Lydie Lane, Christopher M. Overall, Cecilia Lindskog, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Tiannan Guo, Jennifer E. Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz, and Eric W. Deutsch.

    ABSTRACT: Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1−4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

  • 30 Jan 2024 5:54 AM | Anonymous member (Administrator)

    The HUPO Early Career Researcher (ECR) Committee is delighted to welcome Pathmanaban Ramasamy. Keep reading to know more about him!

    Pathmanaban Ramasamy (Paddy) is a junior post-doc in the CompOmics group at Ghent University in Belgium. During his joint Ph.D. program between Ghent University and Vrije Universiteit Brussel, he leveraged his expertise in structural bioinformatics and proteomics informatics to unravel the role of local amino acid interactions in protein folding, fold stability, and the location of post-translational modifications (PTMs). He endeavors to unravel the "where, how, and why" of protein PTMs through a comprehensive large-scale investigation that spans these modifications within sequence, structure, and biophysical contexts.

    He has been extremely active in bringing the MS proteomics and structure communities together at the European scale, investing heavily in an ELIXIR Europe-funded cross-over study between the three key communities: the 3D-BioInfo (protein structure), Intrinsically Disordered Proteins, and MS Proteomics communities. Paddy is enthusiastic about becoming a member of the HUPO-ECR and looks forward to actively contributing to the support of young proteomics researchers through his involvement with HUPO-ECR and YPIC.

  • 30 Jan 2024 5:28 AM | Anonymous member (Administrator)

    Prof. Hong Wang
    Institute Of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, China

    1. What is your current position and affiliation?
      I am presently employed as a Principal Investigator (tenure-track Assistant Professor) at the National Key Laboratory of Blood Science, within the Institute of Hematology & Blood Diseases Hospital at the Chinese Academy of Medical Sciences & Peking Union Medical College. Concurrently, I hold the positions of Director at the Center for Advanced Technologies and Founding Director of the Mass Spectrometry Center at Haihe Laboratory of Cell Ecosystem. 

    2. How would you like your work to contribute to the field of proteomics?
      In my current role at the foremost blood diseases research hospital in China and the innovative Haihe Laboratory of Cell Ecosystem, I aspire to make significant contributions to the field of proteomics. By integrating mass spectrometry-based omics with other advanced technologies, I aim to collaborate closely with clinicians to address complex clinical questions. My goal is to propel these technologies towards translational medicine, facilitating the translation of precision biomarkers and therapeutic targets into practical clinical applications. This approach seeks to bridge the gap between cutting-edge research and real-world patient care. 

    3. What have you found in the HUPO community/congress?
      HUPO serves as my academic home, and participating in the HUPO congress feels akin to a holiday homecoming to reunite with family and friends. Each congress is a source of continual inspiration, fostering valuable collaborations, and exposing me to new technologies that I eagerly incorporate into my work. The sense of community and shared knowledge at HUPO events consistently propels my research forward and enriches my professional journey.

    4. How was your experience/what did it mean to present your work at HUPO?
      Presenting my work at HUPO was an enriching experience, marked by valuable and insightful feedback. The positive reception and recognition of my multidisciplinary efforts within my field provided a significant boost of confidence. This affirmation encourages me to advance further in exploring the novel concept of the blood ecosystem that we introduced, reinforcing my commitment to pioneering work at the intersection of diverse disciplines.
  • 23 Jan 2024 10:56 AM | Anonymous member (Administrator)

    The PSI meeting 2024 will take place from March 18-20th 2024 at the Kyoto University, Japan.

    View event details here.

    The meeting is sponsored by: JPOST (JST-NBDC) and JPDM (JSPS).

    Organizers: Yasushi Ishihama & Shujiro Okuda.

    Are you interested in defining the formats and standards that describe the next generation of mass spectrometry data?

    Then join us at the next HUPO-Proteomics Standards Initiative (HUPO-PSI) Spring Workshop in the beautiful city of Kyoto, to work on to work on developing and updating new and existing standards, such as mzML, mzIdentML, mzSpecLib, mzPAF, mzQC, and the Universal Spectrum Identifier (USI), in the light of new methodologies and technologies.

    The workshop is free to participants, and very hands-on so come prepared to actively engage with this community and present your ideas and use cases. The work of the HUPO-PSI has led to a dramatic increase in the availability of proteomics data in the public domain thanks largely to the wide adoption of open data practices in the field and we look to continue that trend as new methodologies are developed.

    Thanks to our sponsors (HUPO, JPOST (JST-NBDC) and JPDM (JSPS)) we are able to offer a number of generous travel/accommodation grants - please apply for consideration to receive one of these when you register for the meeting.

    Please note that if your interests lie in the field on protein/molecular interactions, this workgroup will meet virtually this year. Register as normal via the link given above and we will finalise timings subject to the geographic location of participants.

    Program:  The provisional agenda will be posted soon.

    Registration:  Registration for attending the meeting is now open.

  • 10 Jan 2024 8:45 AM | Anonymous member (Administrator)

    The January HUPOST is now available.....check out the latest HUPO 2024 news, ETC Webinars, ECR Manuscript Competition, upcoming events & much more...


  • 05 Jan 2024 5:44 AM | Anonymous member (Administrator)

    The HUPO Early Career Researcher (ECR) Initiative is delighted to welcome Nick Riley and Mahshid Moballegh Nasery.

    Nick Riley is an assistant professor of chemistry at the University of Washington. With a background in mass spectrometry instrumentation, proteomics, and glycobiology from his graduatework with Prof. Josh Coon at University of Wisconsin-Madison and his postdoctoral work with Prof. Carolyn Bertozzi at Stanford University, he now leads a research program focused on innovative bioanalytical and chemical biology technologies to investigate essential principles of glycocode regulation and dysregulation. Nick has been involved with HUPO and US HUPO for a number of years and is excited to join the HUPO ECR committee to support the vibrant and supportive communities that help early career scientists build their scientific careers in proteomics research.


    Mahshid Moballegh Nasery pursued a diverse academic journey, beginning with a Bachelor's in Chemistry and delving closer into biology with a Master's in Medical Toxicology, where her focus on cancer led to publications in articles and a chapter book. Her passion for proteomics started to grow as she attended her proteomics course and attended an ECR day meeting! Currently engaged in research at the University of Debrecen, under the supervision of Dr. Eva Csosz. Her recent membership in YPIC (Young Proteomics Investigators Club) reflects her eagerness to expand her network and engage actively with fellow proteomics scientists. She aims to deepen her involvement in various activities, leveraging her multi-disciplinary background, to contribute meaningfully to the scientific community. Driven by a thirst for knowledge and a desire to make impactful contributions, Mahshid is passionate about exploring within the vibrant realm of proteomics and biochemistry.

  • 05 Jan 2024 5:27 AM | Anonymous member (Administrator)
    Dr. Johannes Bruno Müller-Reif
    (Max Planck Institute of
     Biochemistry, Germany) presented his work Immobility-associated Thromboprotection is Conserved across Mammalian Species from Bear to Human in a plenary session at HUPO 2023 in Busan, South Korea

    Dr. Johannes Bruno Müller-Reif is a project leader and head of the Pediatric Proteomics Group at the Max Planck Institute of Biochemistry (MPIB). During his doctorate with Prof. Matthias Mann, he focused on extending proteomics across the tree of life. Following his PhD, he joined the proteomics start-up OmicEra, where he significantly contributed to high-throughput proteomics methods for biomarker discovery and clinical research. Concurrently, Dr. Müller-Reif maintained a relationship with MPIB as a guest scientist, and his growing expertise led him to establish a research group with focus on the intersection of mass spectrometry-based proteomics and pediatrics.

    Dr. Müller-Reif’s research is multifaceted. A cornerstone of his work involves applying mass spectrometry-based proteomics to large patient cohorts to enhance biomarker discovery. In this capacity, he co-leads the MOMI cohort’s plasma proteomics efforts to address adverse pregnancy outcomes, supported by the Bill and Melinda Gates Foundation. He also focuses on the utilization of proteomics for investigating rare pediatric diseases. Furthermore, Dr. Müller-Reif pioneers the use of proteomics in specialized applications such as platelet biology and studying organisms inaccessible through conventional methods. This innovative approach not only exemplifies the practical versatility of proteomics but also ties back to his doctoral research on the proteome landscape of the kingdoms of life.

    Interview with  Dr. Johannes Bruno Müller-Reif 

    What is your current position and affiliation?
    I am a project group leader (a position somewhat between postdoc and group leader) at the Max Planck Institute of Biochemistry within the group of Matthias Mann.

    How would you like your work to contribute to the field of proteomics?
    I currently focus on clinical mass spectrometry-based proteomics and nearly any project I am working on involves patient samples or is a direct collaboration with clinicians. I would like to continue employing this powerful method to uncover biological mechanisms and better understand diseases, which ultimately will benefit patients with better treatments. In the best case scenario, this leads for example to the discovery of novel biomarkers or therapeutic targets, but also a better functional understanding without the identification of distinct single biomarkers is a step in the right direction. Biomarker discovery is often done with large patient cohorts and I hope to contribute to the field by enabling such studies from a technical perspective and providing the community with unique datasets. In parallel to this work, I would like to transform proteomics from a method for biomarker discovery by retrospective analysis to a tool for pro- and diagnostics in the future.

    What have you found in the HUPO community/congress?
    I had the chance to attend the HUPO world congresses two times so far. I found it to be a perfect intersection of different interest groups forming a thriving community between biological expertise and technical solutions.

    How was your experience/what did it mean to present your work at HUPO?
    Having been invited to the ECR manuscript competition to HUPO in Busan to present my work meant a lot to me. Sharing the excitement about new findings is definitely a driver of motivation for me to work as a scientist and being given the opportunity to do so in such a venue has been a major pleasure. I received a plethora of positive feedback from this wonderful community, which is truly motivating.



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