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  • HUPO ECR Welcomes New Member

    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.

  • Interview with 2023 HUPO ECR Manuscript Competition Finalist: Dr. Hong Wang

    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.

  • HUPO Proteomics Standards Initiative (PSI) Meeting 2024

    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.

  • HUPOST January 2024

    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...


  • HUPO ECR Welcomes New Members!

    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.

  • Interview with 2023 HUPO ECR Manuscript Competition Winner: Johannes Bruno Müller-Reif

    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.

  • ETC Webinar Series: Reverse Phase Protein Array (RPPA) Applications: Molecular Profiling and Predicting Response to Targeted Therapies

    04 Jan 2024 4:38 PM | Anonymous member (Administrator)
    DATE: Wednesday, March 20, 2024
    TIME: 2pm PST / 5pm EST / 10pm CET
    LOCATION:  Zoom (link to follow upon registration)
    SPEAKER:  Rosa Isela Gallagher, PhD

    REGISTER HERE

    WEBINAR DESCRIPTION:

    RPPA is a high-throughput protein array technology that simultaneously measures hundreds or thousands of samples on glass slides with high precision and reliability, using specific antibodies. RPPA and mass spectrometry-based protein profiling are complementary technologies for protein profiling. In attending this webinar, attendees will learn about RPPA's high-throughput capabilities and laser-captured microdissection technology. They will understand how these technologies precisely measure protein expression, modifications, and phosphorylation in tumor cells.

    WHAT ATTENDEES WILL LEARN:

    RPPA Technology Overview: Understand the high-throughput nature of RPPA for simultaneous analysis of numerous samples with minimal amounts. And explore how RPPA measures protein levels and modifications, offering a detailed molecular profile of tumor cells. Clinical Applications: Learn how RPPA and LCM aid in accurate diagnosis and prognosis, particularly in cancer, influencing clinical decision-making. Understand RPPA's role in predicting responses to targeted therapies, shaping the future of personalized medicine.

    CLINICAL APPLICATIONS:

    Learn how RPPA and LCM aid in accurate diagnosis and prognosis, particularly in cancer, influencing clinical decision-making. Understand RPPA's role in predicting responses to targeted therapies, shaping the future of personalized medicine.

    SPEAKER BIO:

    Dr. Rosa Isela Gallagher obtained her Ph.D. in Cell and Molecular Biology from GMU in 2019. She has accumulated more than 15 years of expertise in Reverse Phase Protein Array (RPPA) and Laser Capture Microdissection (LCM) technologies and is currently a Senior Research Scientist in the Center for Applied Proteomics and Molecular Medicine, led by Drs. Lance Liotta and Emanuel Petricoin III, the inventors of both technologies. RPPA is a high-throughput, antibody-based protein array technology capable of conducting assays on small amount of materials on thousands of samples simultaneously. This platform measures protein expression levels and modifications, including phosphorylation. Dr. Gallagher’s current research focuses on the molecular profiling of tumor cells utilizing LCM and RPPA to investigate unique signaling pathway profiles and new disease mechanisms to guide diagnosis, prognosis, and targeted therapeutics.

    REGISTER HERE

  • HUPOST December 2023

    08 Dec 2023 6:23 PM | Anonymous member (Administrator)

    The December HUPOST is now available.....check out the ETC webinars, HPP Chair & Co-chair nominations, C-HPP updates, upcoming events & a farewell message from HUPOST editor Ben Garcia...

  • ETC Webinar Series: Past, Actual, and Future Directions of Trapped Ion Mobility Time of Flight Mass Spectrometry (TIMS-TOF-MS)

    08 Dec 2023 5:02 PM | Anonymous member (Administrator)

    DATE: Wednesday, February 21, 2024
    TIME: 7am PST / 10am EST / 4pm CET
    LOCATION:  Zoom (link to follow upon registration)
    SPEAKER:  Oliver Raether


    WEBINAR DESCRIPTION:

    Trapped ion mobility spectrometry (TIMS) is a powerful analytical technique that separates and characterizes gas-phase ions based on their mobility in a buffer gas. TIMS has been widely applied in various fields, such as proteomics, metabolomics, lipidomics, and pharmaceutical research. It offers sensitivity, speed, and resolution for complex and challenging samples.

    LEARNING OBJECTIVES:

    In the first part of this webinar, you will learn about the history of the TIMS research and development, including the chronological launch of the different timsTOF instruments and SW capabilities by Bruker. You’ll learn about the differences and similarities of the timsTOF instruments, the possible upgrade paths and software options.

    In the webinar, you will also learn about the different data-independent acquisition (DIA) mass spectrometry methods currently used in proteomics and how new approaches benefit from the additional ion mobility dimension and new acquisition modes.

    Finally, in the third part of this webinar, you will learn about some of the future approaches that are currently under development for the TIMS technique, such as TIMS gas phase fractionation and filtering. This is a novel setup that uses two or three TIMS analyzers in a row to separate and isolate different regions of the m/z vs 1/K0 space. This can increase the selectivity and sensitivity of the TIMS technique, and improve applications and workflows especially for heterogeneous proteomics samples. You will see how these methods work, and what are the advantages and challenges of implementing it.

    SPEAKER BIO:

    Oliver Raether is Research and Development Manager at Bruker Daltonics in Bremen. He received his M.Sc. in engineering from the Hamburg University of Technology (1995). Over the past nearly three decades he and his colleagues have developed orthogonal time of flight mass spectrometers including since 2010 the timsTOF product line. He has produced 14 peer reviewed journal articles and is inventor/co-inventor of 71 patents in the field of mass spectrometry and, more recently, ion mobility spectrometry (h-index 13). His awards include the HUPO Science and Technology Award for contributions on Trapped Ion Mobility Mass Spectrometry Instrumentation (2020).

    REGISTER HERE

  • ETC Webinar Series: Why Size Matters: Revolutionizing Protein and Peptide Detection with Ion Mobility

    08 Dec 2023 4:56 PM | Anonymous member (Administrator)

    DATE: Wednesday, January 24, 2024
    TIME: 6am PST / 9am EST / 3pm CET
    LOCATION:  Zoom (link to follow upon registration)
    SPEAKER: Daniel DeBord, PhD

    WEBINAR DESCRIPTION:

    Protein identification is of fundamental importance in many areas of proteomics. Its applications include determining the presence or absence of an expected protein in a sample of interest, identifying an unknown protein present in a biological sample, and identifying a protein responsible for biochemical activity in an isolated protein fraction. In some cases, mass spectrometry or affinity-based methods may be suitable options, but these methods can face substantial challenges. Scientists need the ability to identify and measure peptide modifications, structures, and impurities more definitively and faster. Driven by structures for lossless ion manipulation (SLIM) technology, the MOBIE® instrument’s high-resolution ion mobility mass spectrometry platform separates and identifies the most challenging molecules with unprecedented resolution without compromising speed. By combining the MOBIE® platform’s high-resolution ion mobility mass spectrometry (HRIM-MS) data with liquid chromatography, more accurate separation and identification of impurities and posttranslational modifications (PTMs) can be achieved, reducing run times and costs.

    LEARNING OBJECTIVES:

    1. Attendees will learn Attendees will learn about (1) separation science, including SLIM (structures for lossless ion manipulation) and high-resolution ion mobility (HRIM); (2) the trade-off between speed, resolution, and reproducibility; and (3) accuracy for targeted lipidomics, peptide characterization, glycan analysis, PFAS, and many other workflows.
    2. Why Attend?  AAttendees will uncover insights into how to incorporate HRIM into traditional analytical workflows and where the technology is used to answer clinical questions.

    SPEAKER BIO: 

    Daniel currently serves as the Vice President of R&D for MOBILion Systems, Inc. In this role, he leverages his 15 years of experience developing novel analytical instrumentation to address challenges across a range of application spaces. Daniel received a BS in Chemistry from Campbell University and a Doctorate in Analytical Chemistry from Texas A&M University. Prior to starting work with MOBILion, he served as the Chemistry Manager and lead developer for 1st Detect Corporation, a company that develops miniaturized mass spectrometry-based detection systems for a variety of markets. Daniel also worked as a staff Research Scientist and Associate Director of the Mass Spectrometry Facility at Florida International University and as an LC‒MS chemist for BASF. For the past 10 years, Daniel has focused on developing ion mobility technologies such as trapped ion mobility spectrometry (TIMS) and structures for lossless ion manipulation (SLIM) and exploring how these new techniques can be coupled with traditional LC‒MS instruments to access higher performance in fields such as proteomics and biopharma characterization.

    REGISTER HERE