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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.

FEATURED ARTICLES


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  • 28 May 2021 3:38 PM | Anonymous member (Administrator)

    Written by Eric Deutsch, Institute for Systems Biology USA; David L. Tabb, Pasteur Institute, Department of Structural Biology and Chemistry France; Sandra Orchard, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) UK; Juan Antonio Vizcaíno European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) UK; Andrew R Jones, Institute of Systems, Molecular and Integrative Biology UK

    The Proteomics Standards Initiative (PSI) was formed as a HUPO working group back in 2002, with an aim to improve data sharing and standardisation in proteomics. At that time, proteomics was a rapidly developing technique, and the concept of sharing data in support of publications was still in its infancy. Most proteomics articles reported tables of protein identifications or quantitative values in PDF format, inhibiting their import into other software. Visualizing peptide-spectrum matches was rare, preventing critical assessment of PSM quality. The PSI’s primary aims were i) to develop data standards that would enable the submission of data (raw and/or processed) to public databases or for interchange between software, improving transparency and data re-use; ii) to develop “reporting requirements” indicating the types of information that should be recorded e.g. in a Methods section or database entry, to allow critical interpretation of results; and iii) to help foster a culture of data sharing, including developing software to make sharing easier. The PSI has had major impact in the past 19 years, where we are now in a situation where most proteomics data sets are readily available, in formats that support critical assessment of results, and allow for data re-purposing.

    The PSI’s activities have largely been divided in two main branches - molecular interactions (MI) and mass spectrometry (MS)-based workflows, with the main highlights being the development of widely used standard formats (https://www.psidev.info), and international cooperation for data submission and access, coordinated through the ProteomeXchange (http://www.proteomexchange.org/) and IMEx (www.imexconsortium.org) Consortia. These developments have been essential in the context of the HUPO Human Proteome Project.

    The current make-up of the PSI involves six working groups - MS, Proteome Informatics, MI, Protein Modifications (MOD), Quality Control (QC) and a recent addition: Intrinsically Disordered Proteins (IDP). We also have a group dedicated to coordination of activity with parallel efforts in metabolomics.

    The roster of current PSI leadership is available at https://www.psidev.info/roles. We would like to bring to the attention of the proteomics community that are planning refresh roles for working group Chairs and co-Chairs in 2021, particularly in the Proteome Informatics area. We are also searching for a new PSI Editor. If you would like to nominate yourself or someone else for a role as Chair, co-Chair or other role within a working group, please email to andrew.jones@liverpool.ac.uk to start the conversation. We would expect that individuals would have had some involvement before in PSI activities, but of course we are a fully open organisation, and always welcome new members.

    In March 2021, we held our annual PSI Spring Workshop (fully online for the second time). The main focal points of the meeting were:

    MI: This track (www.psidev.info/groups/molecular-interactions) has been responsible for the creation and maintenance of several different data exchange formats (PSI-I XML2.5, PSI-MI XML3.0, MITAB2.5-2.8, MI-JSON) and the accompanying controlled vocabulary (PSI-MI CV), and this year focused on a number of new use cases, modeling these to the existing standards to ensure that these were still fit for purpose. Use case examples included contextual interactions, the interactome of a specific cell or tissue type and dynamic interactions, the sequential changes in the composition of these interactome over time or in response to an agonist or inhibitor. We agreed upon a major refactoring of the genetic interaction branch of the PSI-MI CV and discussed methods for linking entities derived from the same gene e.g. proteins and their originating mRNAs, in a network. Finally, we held the annual IMEx Consortium meeting, with participating databases and data users in attendance. We are open to welcoming new members interested in curating molecular interactions or in further developing data standards.

    MS/PI: This track touched on many different topics in an effort to gather input from those participants who do not regularly participate in the ongoing development. We began with a session exploring how the PSI might contribute to the emerging field of non-MS affinity-based workflows, and then moved on to the nearly-ratified Universal Spectrum Identifier (USI) standard. We discussed the ProForma 2.0 in-development standard for proteoform and peptidoform notation, and the PROXI application programming interface for programmatically exchanging proteomics information between ProteomeXchange resources. We explored a proposed extension of the existing mzIdentML and mzTab standards for glycoproteomics, and a proposed format (called SDRF-Proteomics) for the annotation of the relationship between samples and data files in proteomics datasets, aiming to capture the experimental design. We finished the workshop with discussions on the emerging PSI Spectral Library Format (mzSpecLib), an update of mzTab for proteomics, and a binary version of mzML called mzMLb. The MS/PI working group aims to ratify and release several of these formats in the coming year and welcomes additional participation. Several MS/PI members also participated in efforts in the MOD working group, to produce updates to the PSI modification controlled vocabulary that is used across a range of standards in both the MI and MS spaces.

    QC: Across all of biological MS, efforts to increase repeatability and reproducibility of experimentation has become a priority. Communicating quality information in a standardized way has the potential to improve interaction between quality metric-generating software (e.g. reporting the fraction of all MS/MS scans being identified in an LC-MS/MS experiment) and quality decision-making frameworks (e.g. recognizing an LC-MS/MS experiment is an outlier). The mzQC format specification should shortly be released for public comment. It is distinctive for being one of the first HUPO-PSI formats to employ lightweight JSON notation rather than XML, while continuing to define the terms employed in mzQC in a CV.

    IDP: The recently formed Intrinsically Disordered Proteins group (https://www.psidev.info/groups/intrinsically-disordered-proteins), is aimed with understanding and sharing data on disordered regions of proteins, particularly developing annotation standards for structural and structure-function attributes. The group is starting to work on reporting guidelines, and data standards for describing annotations in tab-based and XML formats.

    What all of these efforts have in common is that proteomics (and metabolomics) researchers need ways to communicate their results in a way that is verifiable and trustworthy. Already we have seen a sizable impact from these efforts; analytical chemists that use SCIEX instruments can post to a repository both mzML-formatted data and WIFF files, for example, to ensure that laboratories that do not have access to vendor software can still make use of their MS experiments. Another example is that bioinformatics researchers seeking to optimize the classification of PSMs into accepted and rejected collections can work from the mzIdentML PSMs reported for a wide variety of database search algorithms in thousands of experiments.

    The PSI continues to make rapid progress in its mission to facilitate data sharing and access in the proteomics community, but needs additional participation from the community at all levels to maintain momentum. In addition to the need to support novel approaches and workflows in the field, an additional point of interest is the integration of proteomics with other omics data types and approaches. Will you join us?

  • 30 Apr 2021 1:30 PM | Anonymous member (Administrator)

    Written by Henry Rodriguez, National Cancer Institute, USA

    Born out of the Human Genome Project, the field of genomics evolved with phenomenal speed into a dominant scientific force and opened new avenues to discover cures to diverse diseases… especially in oncology. And as quickly as genomics grew, today we again find ourselves in the midst of a new revolution in science. This new revolution is enabled by the convergence of genomics with proteomics, whose collective goals are to achieve a comprehensive understanding of the information encoded in the genetic material of organisms and how it directs the organization and function of living systems.

    What we are now seeing in proteomics is a science discipline that seems to be at an inflection point, that is the result of widespread technological advances (analytical and computational, standardized workflows ensuring data rigor and reproducibility, and data sharing with the public) and an acknowledgement that genomic data alone do not always provide sufficient insights into the molecular classification of cancer in modern medicine. The outlook for proteomics has brightened substantially. And while today we assess these advances with optimism (and pessimism) as it pertains to precision medicine, the road taken to where proteomic advances are today has not been easily traveled.

    At the U.S. National Cancer Institute, National Institutes of Health, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) was established to address these advances in the field of oncology. Its initial goal was to standardize proteomic methods to ensure rigor and reproducibility of large-scale protein measurements among laboratories, done in coordination with the U.S. Food and Drug Administration and the American Association for Cancer Research. Having achieved this goal, CPTAC then applied its standardized proteomics workflows to three previously genomically characterized tumor types from TCGA (proteogenomics), that revealed additional layers of molecular information not possible through genomics alone. The success of these activities by demonstrating the benefit and need of integrating proteomics with genomics to produce a more unified understanding of cancer, led the NCI to expand CPTAC’s proteogenomics tumor characterization program and for the very first time, to partner with NCI-supported clinical trials.

    The reality is that proteomics and genomics are not competitors. Rather, they are partners. Together, along with other “omics” approaches, they promise to reveal molecular patterns spanning multiple layers of biology and informing new approaches to diagnostics and therapeutics. These complementary approaches stand to make precision medicine a reality.

    The CPTAC program took a risk and in doing so pioneered the emerging field of cancer proteogenomics, while perhaps more importantly restoring interest and enthusiasm in the use of proteomics in the cancer community. To commemorate the advances in science made by the CPTAC program to accelerate our understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, and the program’s commitment to creating public resources (data, assays, and reagents [antibodies]) that are utilized by the cancer research community, Cell Press has created an online space dedicated to archiving CPTAC research (https://www.cell.com/consortium/CPTAC) that has and will be published in its family of journals. Also included below are papers that are a collaboration between CPTAC and the International Cancer Proteogenome Consortium (ICPC; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002958). Collectively these papers provide strong resource-based frameworks to better understand a range of human cancers through the lens of precision oncology and will be valuable in informing effective treatment options.

    Furthermore, to understand where colleagues and I see cancer research headed in the next decade, a perspective article was recently published where we examine cancer through the lens of comprehensive molecular characterization of tumors from cancer patients. In this article (https://www.cell.com/cell/fulltext/S0092-8674(21)00285-3) titled “The Next Horizon in Precision Oncology: Proteogenomics to Inform Cancer Diagnosis and Treatment,” we describe the significant contributions of The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) to multidisciplinary collaborative team science and precision oncology, and make the case that proteogenomics needs to be fully integrated into clinical trials and patient care. This approach of genomic and proteomic markers, we believe, will further enable precision oncology to deliver the right cancer treatment to the right patient at the right dose and at the right time.

  • 30 Apr 2021 12:59 PM | Anonymous member (Administrator)

    Written by Emily Hashimoto-Roth, University of Ottawa, Canada

    The month of May will see the start of the Early Career Research Initiative’s (ECR) new interactive panel series! This series, organized in collaboration with the EuPA’s Young Proteomics Investigators Club, will be hosting its inaugural panel discussion on May 17th at 7PM EDT (GMT-4/New York Time), 4PM PDT (GMT-7/Los Angeles Time) and 7 AM CST (GMT+8/Taipei Time) on May 18th. Guests will have the opportunity to hear from and ask questions to our wonderful speakers, Dr. Yu-Ju Chen (Academia Sinica, Taiwan and HUPO President), Dr. Renã A. S. Robinson (Vanderbilt University, USA) and Dr. Robert Rivers (National Institutes of Health, USA), as they discuss the effective promotion of diversity in proteomics. Chairing the inaugural session will be the ECR’s Emily Hashimoto-Roth (University of Ottawa, Canada). To register, please use the following link: https://us06web.zoom.us/meeting/register/tZcsfuugrT8qG9HJGsyNWCzlt9d17pwedSWZ. Register early! There is a limited attendance! Get your questions ready, we cannot wait to see you there!


    Dr. Yu-Ju Chen, Academia Sinica, Taiwan and HUPO President



    Dr. Renã A. S. Robinson, Vanderbilt University, USA

     


    Dr. Robert Rivers, National Institutes of Health, USA




  • 29 Jan 2021 1:41 PM | Anonymous member (Administrator)

    By Michelle Hill, QIMR Berghofer Medical Research Institute, Brisbane, Australia

    It has been a pleasure to serve as HUPOST editor and HUPO Secretary General for the past 2 years. I would like to thank our staff editor Amanda, HPP and ECR news co-ordinators for their continued dedication to HUPOST and the HUPO community. A highlight for 2020 was the “Proteomics in Action” article series that showcased global proteomics uses in everyday life from forensics, clinical diagnostic, drug development to archeology and marine science. Particular thanks go to Stephen Pennington for his enthusiasm and support, as well as all contributors and the people featured.

    I now pass the reins of HUPOST editor to Ben Garcia. Ben is currently the John McCrea Dickson, MD, Presidential Professor in the Department of Biochemistry and Biophysics, and Director of Quantitative Proteomics at the University of Pennsylvania School of Medicine. His research interests include applying mass spectrometry based proteomics for understanding epigenetic mechanisms in human disease, presenting his work at many HUPO World Congress meetings in the past. Ben has been on the Board of Directors of the United States HUPO since 2011, and served on the HUPO Council since 2016. In addition to his recent election to the HUPO Executive Committee as Member-at-Large, Ben has also joined the Marketing & Membership Committee. Hence, he is well-placed to ensure HUPOST fulfils both HUPO member communication needs and marketing strategies.

    All HUPO members can submit proteomics related announcements (workshops, courses, job openings) for consideration for HUPOST, which is sent out monthly to the HUPO mailing list. If you have any ideas for HUPOST, please reach out to Ben via office@hupo.org.

  • 28 Jan 2021 4:44 PM | Anonymous member (Administrator)

    Emily Hashimoto-Roth is a graduate student at the University of Ottawa pursuing a Master’s in Biochemistry specializing in Bioinformatics, under the co-supervision of Dr. Mathieu Lavallée-Adam and Dr. Steffany Bennett. Having obtained an H.B.Sc. in Biopharmaceutical Science at the University of Ottawa, her current research focuses on the design of statistical models and machine learning algorithms to mine and analyze protein-protein interaction datasets. She is a trainee within the NSERC-CREATE Metabolomics Advanced Training and International Exchange Program (MATRIX), further diversifying her graduate studies. In addition to her studies, she is the Director of Communications for a Canadian federal non-for-profit organization called Pulsar Collective, whose mission is to improve gender equality in STEM. She is also a member of the Canadian National Proteomics Network’s Operations Management Team, which works to advance the proteomics field by fostering a community for researchers to meet and collaborate.

  • 28 Jan 2021 4:34 PM | Anonymous member (Administrator)

    Mathieu Lavallée-Adam, ECR Co-Chair, University of Ottawa, Canada

    The HUPO Early Career Researcher (ECR) Initiative is proud to announce that Dr. Ruth Huttenhain and Dr. Mathieu Lavallée-Adam have been newly elected as its Co-Chairs. The ECR initiative also thanks Dr. Justyna Fert-Bober, founding member of the HUPO ECR Initiative and exiting Chair, for spearheading the activities that the ECR Initiative is now known for, such as the HUPO Mentoring Day, Manuscript Competition and Ph.D. Poster Competition. “I am happy to leave the leadership of the HUPO ECR Initiative in such good hands. I am convinced that Dr. Huttenhain and Dr. Lavallée-Adam will grow the initiative and build an environment that will foster new collaborations and bring new ideas to life,” declares Dr. Fert-Bober. Dr. Huttenhain, who has, among other things, organized the HUPO ECR manuscript competition in the past, says: “In my role as a Co-Chair of the HUPO ECR Initiative, I am particularly excited about growing a larger community of early career scientists in proteomics with the ultimate goal to provide guidance for taking the next steps in their careers. I will also be honored to represent the ECR Initiative in the Organizing Committee of the HUPO World Congress and to advocate for a program that provides visibility for early career scientists and highlights their scientific contributions.” Finally, Dr. Lavallée-Adam, who has been organizing last year’s mentoring sessions at HUPO CONNECT and coordinating ECR’s HUPOST publications adds: “Early career scientists are more diverse than ever and the HUPO ECR Initiative must help them exploit their full potential. I look forward to building upon our current portfolio of activities and constructing new initiatives to showcase proteomics rising stars and provide them the tools to be more competitive on the job market.”

    You will find below short bios of Dr. Huttenhain and Dr. Lavallée-Adam, who are both recipients of the Proteomics Highlight of the Year by an Early Career Researcher Award given at the 2018 Human Proteome Organization World Congress.

    Ruth Huttenhain
    Ruth Huttenhain is an Assistant Professor at the University of California, San Francisco (UCSF) in the Department of Cellular and Molecular Pharmacology. She obtained a Pharmacy degree from the University of Bonn and a PhD from ETH Zurich, Switzerland, where she developed high-throughput, large-scale targeted mass spectrometric approaches. During her postdoc at UCSF, Ruth extended her expertise in quantitative mass spectrometry to study dynamics of protein interaction networks. She pioneered a proximity labeling-mass spectrometry approach that simultaneously captures the precise temporal remodeling and spatial organization of proximal protein networks. The research of Ruth’s research group at UCSF focuses on characterizing protein interaction and signaling networks to understand the biology underlying the development of psychiatric disorders and the sensing and transmission of pain.



    Mathieu Lavallée-Adam
    Mathieu Lavallée-Adam is an Assistant Professor at the University of Ottawa in the Department of Biochemistry, Microbiology and Immunology and is affiliated to the Ottawa Institute of Systems Biology. He obtained a B.Sc. in Computer Science and a Ph.D. in Computer Science, Bioinformatics option, from McGill University. He then performed his postdoctoral research at The Scripps Research Institute. His research focuses on the development of novel statistical and machine learning algorithms for the analysis of mass spectrometry-based proteomics data and protein-protein interaction networks. He also designs computational methods mining proteomics datasets for biological information through their integration with genomics data. Dr. Lavallée-Adam is a recipient of the John Charles Polanyi Prize in Chemistry, recognizing the impact of his bioinformatics algorithms on the mass spectrometry community. He is also a member of the Board of Directors of the Canadian National Proteomics Network (CNPN), in which he mentors a group of early career researchers in the establishment of activities for the Canadian Proteomics community.

  • 12 Jan 2021 3:24 PM | Anonymous member (Administrator)

    Mathieu Lavallée-Adam, University of Ottawa, Canada

    Blandine Chazarin is a postdoctoral scientist in Dr. Jennifer Van Eyk’s laboratory at Cedars-Sinai hospital in Los Angeles, California. After four years in Paul Sabatier University in Toulouse studying Biology, Blandine explored proteomics for a year before beginning a Ph.D., in which she used mass spectrometry to better understand hibernating brown bear physiology, with the goal to discover new therapeutic approaches for muscle atrophy. In October 2019, she obtained her Ph.D. in LSMBO lab in Strasbourg, France. Blandine has also been President of the Youth Club of the Proteomic French Society for three years and was the organizer of yearly meetings dedicated to young scientists in proteomics. She is now involved in the Postdoctoral Scientist Society at Cedars-Sinai and continues to use mass spectrometry to answer biological questions.

  • 12 Jan 2021 2:46 PM | Anonymous member (Administrator)

    Professor Vera Ignjatovic, Chair, HUPO Marketing and Membership Committee

    Vera is a Senior Principal Research Fellow and a group leader of the Haematology team at the Murdoch Children’s Research Institute in Melbourne, Australia. She lead a highly productive, internationally competitive research team in the field of paediatric thrombosis and haemostasis (aka kids' blood). Her research efforts include the use of proteomic studies in the paediatric setting, where she established for the first time the concept of Developmental Proteomics.

    As a lifelong learner she recently completed a Global Executive MBA at the Monash University in Melbourne, an experience that included training in strategic marketing; executive leadership; corporate finance, governance and strategy; as well as innovation and entrepreneurship, and commercialisation of technology. The learnings from the Global Executive MBA and exposure to the world outside of the immediate research environment will be of advantage in her role as the incoming Chair of the HUPO Marketing and Management Committee.

    Whilst the 2021 Marketing and Membership committee is in its infancy, Vera is very happy to announce 5 new committee members, James Waddington (Co-Chair), Conor McCafferty (PhD representative), Jennifer Geddes-McAlister, Benjamin Garcia and Lennart Martens. She very much looks forward to working with all HUPO Marketing and Membership Committee members to increase the visibility of the HUPO brand in 2021 and beyond.

  • 26 Nov 2020 6:01 PM | Anonymous member (Administrator)

    Mathieu Lavallée-Adam, University of Ottawa, Canada

    Emily Hashimoto-Roth is a graduate student at the University of Ottawa pursuing a Master’s in Biochemistry specializing in Bioinformatics, under the co-supervision of Dr. Mathieu Lavallée-Adam and Dr. Steffany Bennett. Having obtained an H.B.Sc. in Biopharmaceutical Science at the University of Ottawa, her current research focuses on the application of statistical models and machine learning algorithms to mine and analyze protein-protein interaction datasets. She is a trainee within the NSERC-CREATE Metabolomics Advanced Training and International Exchange Program (MATRIX), further diversifying her graduate studies. In addition to her studies, she is the Director of Communications for a Canadian federal non-for-profit organization called Pulsar Collective, whose mission is to improve gender equality in STEM. She is also a member of the Canadian National Proteomics Network, which works to advance the proteomics field by fostering a community for researchers to meet and collaborate.

  • 30 Oct 2020 11:43 AM | Anonymous member (Administrator)

    Once again this year, the HUPO Early Career Researcher (ECR) initiative in collaboration with the EuPA Young Proteomics Investigators Club (YPIC), organized mentoring activities during HUPO Connect 2020, where early career researchers could hear from and interact with leaders of the Proteomics field. This year, the mentoring sessions were integrated in the main program of the congress at different time slots to allow people across to globe to connect and exchange. In the first session, trainees and supervisors learned how to get the best out of a mentor-mentee relationship with Lisa Jones (University of Maryland) and Brandon T. Ruotolo (University of Michigan). In the second session, Benjamin Garcia (University of Pennsylvania), Ruth Huettenhain (University of California San Francisco), and Justyna Fert-Bober (Cedars-Sinai) discussed work-life balance and the challenges faced during the COVID-19 pandemic. Finally, in the last session, Bernard Delanghe (Thermo Fisher Scientific) and James Anson (Molecular Omics) gave insights about the transition from academia to the industry.

    With over 200 attendees participating in all three sessions, the 2020 mentoring activities show the greatest attendance since the beginning of mentoring activities at the HUPO conferences. We thank all mentors for sharing their experience with mentees. We also thank all attendees for their participation and for engaging in stimulating, thought provoking discussions during the congress.

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