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


  • 28 Feb 2018 10:42 AM | Anonymous

    Lennart Martens, Ghent University, Dept of Biochemistry, Belgium

    Proteomics bioinformatics was recently accepted as a formal Community in the European ELIXIR Bioinformatics Research Infrastructure, and currently consists of thirteen members: Germany, Belgium, Czech Republic, Denmark, France, Italy, Netherlands, Sweden, Switzerland, Ireland, UK and EMBL-EBI.

    To learn more about what this means for the field, HUPOST spoke with Dr. Juan Antonio Vizcaíno (EMBL-EBI), Prof. Oliver Kohlbacher (University of Tuebingen), and Prof. Lennart Martens (Ghent University and VIB), three of the founders of the newly minted ELIXIR Community, about what this means for proteomics.

    HUPOST: What exactly is ELIXIR?

    JAV: ELIXIR is a recently created European Research Infrastructure (ESFRI) for life sciences data. It was founded in 2014 as a way to raise awareness in the research community about the importance of European data resources and bioinformatics tools, which increasingly act as basic building blocks for research in the field.

    OK: In that vein, ELIXIR aims to establish standards, bring researchers together, and enable international collaboration on these topics. And to enable all this, there is some funding available as well.

    LM: ELIXIR is organized around the central ELIXIR Hub at EMBL-EBI, which is connected to a network of national nodes in 21 European countries at present, with in turn act as liaisons to 180 research organizations. So ELIXIR is in its essence a large-scale European research network for bioinformatics research infrastructure.

    HUPOST: Why is a Proteomics Community within ELIXIR important?

    JAV: The creation of formal Communities (formerly known as ‘use cases’) within ELIXIR is meant to highlight special interest subgroups that focus on a mature application domain within the life sciences.

    LM: So having a Proteomics Community brings three benefits: first, it recognizes the importance of proteomics, and of proteomics bioinformatics in the life sciences in general; second, it provides a means for the European proteomics bioinformatics community to interact between the various nations; and third, it also provides a formal framework to integrate proteomics bioinformatics with other Communities (see here).

    HUPOST: What was needed to establish the Proteomics Community in ELIXIR?

    JAV: First, the ELIXIR Hub asked prominent members in the community to organize a workshop, which served as the catalyst to write a white paper to establish the needs of the community, their contributions and links to other Communities, and their priorities related to the five core ELIXIR platforms: data, tools, compute resources, training, and interoperability.

    OK: The Proteomics Community white paper has been published as open access in F1000Research, and you can find it here. It is worth noting that the same workshop also sparked off similar activities for a separate, but closely connected, metabolomics community in ELIXIR.

    LM: Once the white paper had been published, a formal Community application was submitted, which was then reviewed and approved by the Heads of Node of the different ELIXIR members.

    HUPOST: What has the ELIXIR Proteomics Community already accomplished?

    JAV: We have recently been granted a first Implementation study application, and a second one has been applied for. These Implementation Studies are small-scale collaborative projects in which several national ELIXIR nodes work together towards a common goal, again focused primarily on one of the five ELIXIR platforms.

    LM: And let’s not forget that the PRIDE database has also been named an ELIXIR core data resource, which are European resources deemed to be of fundamental importance to the wider life science community, and for the long-term preservation of biological data (see here). This decision thus recognizes the efforts that the community has been investing in making proteomics data available, as well as the widespread adoption of data sharing practices in the field.

    HUPOST: Seems like you’re off to a good start! What are the next steps for the Proteomics Community?

    JAV: We identified three areas of future activities: improved data processing and analysis pipeline; elucidation of the deep proteome and its integration with multi-omics data; and of course, throughout we need data management and annotation! The details are set out in our the white paper. Of course, these goals are directly relevant to HUPO, and this is no coincidence. European proteomics bioinformatics researchers have after all been very actively involved in several related HUPO initiatives, such as HUPO-PSI and the HPP.

    LM: It’s also relevant to point out that the ELIXIR Proteomics Community is happy to liaise with similar proteomics and proteomics informatics communities outside of Europe. And we really do need to invest some time in the near future to make a nice Community webpage on the ELIXIR website, with our vision, contact details, and plans!

    HUPOST: Thank you for your time, and good luck with the ELIXIR Proteomics Community!

  • 28 Feb 2018 10:39 AM | Anonymous

    Lennart Martens, Ghent University, Dept of Biochemistry, Belgium

    Spring is just around the corner in the Northern Hemisphere, which probably has something to do with a forward looking issue of HUPOST.

    A first forward look concerns the 2018 HUPO World Congress at Orlando, Florida, which will take place from September 30 until October 4th, and for which registration has now been opened! All information can be found on the 2018 HUPO Congress website.

    A second forward look brings us to the newly minted Proteomics Community in the ELIXIR European Bioinformatics Research Infrastructure. If this does not automatically make a lot of sense to you, you should definitely read the HUPOST interview with a few of the founders in this issue!

    And as a third forward look, you will also find the announcement of the 19th Chromosome Centric Human Proteome Project workshop in this issue, which will be held in Santiago de Compostela in Spain in the weekend of June 16-17, 2018 as a companion event to the XII EuPA Congress 2018.

    And in closing, I leave you with this bit of interesting information: Santiago de Compostela has a 1000-year history as one of the main pilgrimage sites in Europe, and remains extremely popular today. So if you see some weary travellers while you’re there, keep in mind that they have just walked hundreds or even thousands of kilometers to get there!

    Cheers, Lennart Martens, HUPOST Editor.

  • 25 Jan 2018 2:32 PM | Anonymous

    Péter Horvatovich, University of Groningen, Netherlands

    Proteins are biologically active biomolecules encoded by genes, which realize the key molecular events of life. The Chromosome-Centric Human Proteome Project (C-HPP), together with the proteomic scientific community, had a successful five years of research progress to identify missing proteins in the human proteome. Missing proteins are those encoded by human genes but with limited or no protein evidence (PE) of translation. The official human proteome database for HUPO is neXtProt, which has collected protein evidences on 87% of human protein coding genes.

    The attention of C-HPP community is starting to pivot towards other aims, including the functional characterization of proteins that have been identified with strong evidences (PE1), but have completely unknown functions. These human protein coding genes are termed uncharacterized (u)PE1 proteins. NeXtProt contains 1200 uPE1 proteins-See complete list in neXtProt here. The C-HPP executive committee encourages C-HPP members and the proteomics community to develop functional analysis of these proteins, with the aim to complete the picture of the function of the human proteome.

  • 25 Jan 2018 1:58 PM | Anonymous

    Fernando Corrales, Centro Nacional de Biotecnología, CSIC, Spain

    One of the main goals of the Biology and Disease Human Proteome Project (B/D-HPP) is to unveil the molecular basis of physiological/pathological processes by the identification of the driver proteins involved. To guide studies in this direction, B/D HPP initiatives have been encouraged to configure lists of popular proteins in their specific areas (highly cited proteins in association with the topic of interest) to generate functional hypothesis and to pave the way for new clinical developments. The 2017 HPP Special Issue published in the Journal of Proteome Research collect two reports highlighting the usefulness of the popular protein approach. These studies demonstrate the principal role of the reconfiguration of one carbon metabolism in the liver during hepatocarcinogenesis and the development of a targeted method to monitor B-type natriuretic peptidoforms that might prove to be useful for the diagnosis and monitorization of heart failure. The development of multiplexed MS-based targeted method to monitor the disease-associated protein/peptides offer new opportunities in the clinical setting. Moreover, a major update of the human plasma proteome that integrates now 3509 proteins was reported. Finally, the in depth analysis of the synaptosomal proteome allowed the association of specific protein expression patterns with social behaviour in patients with schizophrenia. This is an excellent example illustrating the great advantages of establishing joint C- (chromosome 15) and B/D HPP (Brazilian Brain initiative) ventures. The cooperative efforts should guide our next steps in the endeavour of generating a comprehensive human proteome map with all functional annotations needed to decipher the code of life.

  • 05 Jan 2018 10:42 AM | Anonymous

    Fernando Corrales, Centro Nacional de Biotecnología, CSIC, Spain

    The first International Course on Clinical Proteomics, sponsored by HUPO, took place during the week of the 23-27th of October in the University Hospital of A Coruña (Spain). This course had the aim of showing the analytical procedures that are routinely developed in a Hospital, and the applications that proteomics technologies can have in this environment. The course was organized by the Spanish network of proteomic facilities, ProteoRed and HUPO.

    During the mornings, the attendees were integrated into the work of five different areas of the hospital: clinical analysis/laboratory, pharmacy, microbiology, histomorphology/anatomic pathology, and the biobank. These rotations allowed a direct contact with the most common clinical analytical routines of the A Coruña Hospital, a reference centre in Spain with more than 1.400 beds and around 4.800 workers.

    The afternoons were dedicated to lectures on the application of clinical proteomics approaches in the different areas. On Monday, Fernando Corrales (Director of ProteoRed) gave an overview of clinical proteomics, its technologies and strategies. Tuesday was dedicated to applications of proteomics in pharmacy, and Ángel García (president of de Spanish Proteomics Society, SEProt) spoked about the discovery of novel targets and drugs in platelet-related diseases. On Wednesday Connie Jiménez (BD-HPP Cancer Initiative), head of the Oncoproteomics Laboratory of the VMUC-Cancer Center (Amsterdam) described different proteomic strategies in cancer research, including phosphoproteomic approaches and the analysis of liquid biopsies such as CSF and urine. In the Microbiology session on Thursday, Marina Oviaño (Microbiology Department of the Hospital) showed the applications of MALDI-mass spectrometry for the identification of bacteria and the evaluation of antimicrobial resistance that have been implemented in her Department. Finally, Beatriz Rocha (Maastricht Multimodal Molecular Imaging Institute) gave on Friday a lecture on mass spectrometry imaging and the promising translation of this technology into clinical applications.

    The final impression of both students and organizers has been very positive. In the evaluation survey, the students highlighted as the most interesting issue having the opportunity to work in the services of microbiology and clinical analysis of this big hospital. We hope this course will be consolidated as an international reference for clinical proteomics researchers.

    PHOTO: Participants at the 2017 I Clinical Proteomics Course.

  • 05 Jan 2018 10:36 AM | Anonymous

    Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

    On a beautiful sunny November day in Sydney, Australian proteomics practitioners had a first date with pathologists, at The RCPA Introduction to Proteomics in Pathology Course. The one-day course was co-organised by The Royal College of Pathologists of Australasia (RCPA) and The Human Proteome Organisation (HUPO), and included 17 invited lectures.

    The 59 delegates from pathology services, industry, universities and research institutes across Australia crowded The RCPA Professor Alan BP Ng Education Centre in Sydney. Following opening remarks by Associate Professor Peter Stewart (RCPA, organising committee), Professor Mark Baker outlined the Human Proteome Project, and Professor Marc Wilkins gave a lecture on the Principles of Proteomic Methodologies. Perhaps not unexpected, the cancer proteomics was featured in several lectures, including applications in cancer diagnostics (Associate Professor Rosemary Balleine), treatment decisions (Professor Roger Reddell), ProCan Program (Dr Peter Hains), as well as approaches to biomarker discovery (Professor Peter Hoffmann, Associate Professor Michelle Hill, Dr Charlie Ahn). Other topics included Quality Assured Big Data in Pathology (Associate Professor Tony Badrick), Bioinformatics Data Analysis (Professor Terry Speed), Pediome (Associate Professor Vera Ignjatovic), Microbiome (Dr Adam Rainczuk), Cardiovascular Disease (Dr Melanie White), and Personalised Medicine (Professor Ed Nice). The day concluded with panel discussion and drinks mixer.

    The enthusiasm was palpable, with the day being literally the first introduction to proteomics for most of the RCPA members attending the course. Robust discussions ensued on the analytical methods and quality assurance aspects of proteomic technologies, in comparison to pathology standards. With delegates showing a strong interest in marrying proteomics with pathology, it will not be surprising to see some second dates and success stories in the near future. Indeed, the upcoming Australian Association of Clinical Biochemists (AACB) joint Course ‘Assessing the Value of Biomarkers’ with European Federation of Clinical Chemistry and Laboratory Medicine is a timely follow-up opportunity to foster the relationship between proteomic biomarker researchers and clinical implementation.

    A personal highlight for me was meeting some of the (satisfied) clinicians who have submitted samples to the Princess Alexandra Hospital Amyloidosis Centre ( for proteomic typing of amyloidosis. While we recently published the results of our 5-year study (, it is not often that the scientists come face to face with end-users. At the end of a stimulating day, I head home on the late flight with renewed purpose and optimism for clinical applications of proteomics.

    PHOTO credit, The Royal College of Pathologists of Australasia (RCPA). Organizing committee for The Introduction to Proteomics in Pathology Course. From left to right, Prof Mark Baker (HUPO), A/Prof Peter Stewart (RCPA), Prof Rita Horvath (RCPA), Prof Ed Nice (HUPO). 

  • 05 Jan 2018 10:28 AM | Anonymous

    In cooperation with B/D-HPP investigators, the C-HPP Special Issue JPR came out on December 1, 2017, which marks the fifth consecutive edition since the first issue has been published in January 2013. This issue culminates in total 191 papers which are focused on C-HPP initiative and related HPP topics. In this issue, 27 papers address (1) the accurate mapping of human protein parts list, which has been well progressed towards the completion of HPP goals and (2) advances in the proteomic technologies for the broader community (Paik et al., 2017, in Editorial). Those 27 manuscripts are categorized in four subjects: (i) Metrics of Progress and Resources, (ii) Missing Protein Detection and Validation, (iii) Analytical Methods and Quality Assessment, and (iv) Protein Functions and Disease.

    All manuscripts in JPR special issue provided data on missing proteins and other claims for new protein sequences in accordance with the Human Proteome Project Data Interpretation Guidelines (Version 2.1.0 - July 28, 2016) which requires mandatory full submission of LC-MS/MS data to ProteomeXchange. For this special issue the version of neXtProt issued on January 23, 2017 was used, which has confident protein identification for 17 008 human protein coding genes (category PE1) leaving 2 579 human protein coding genes for which evidence at protein levels should be found either using mass spectrometry or other analytical methods (missing proteins with protein evidence level PE2+PE3+PE4) and 572 human genes which are considered to be dubious (protein evidence PE5). Notably, authors report 73 new missing protein detections by mass spectrometry using several approaches. This data is currently being processed by PeptideAtlas and neXtProt and will be available in the next versions of these two resources, expected in January and February 2018, respectively. The 2018 special issue will be continued and was announced with a ‘Call for Papers’ in JPR, with deadline to submit manuscripts of May 31, 2018. This issue will also cover both C-HPP and B/D-HPP subjects. For this special issue the version of neXtProt that will be issued on February will serve as a reference. Read the December 2017 issue of the Journal of Proteome Research here.

  • 30 Nov 2017 2:03 PM | Anonymous

    Lennart Martens HUPOST Editor, Ghent University, Belgium

    The focal point of 2017 was undoubtedly the HUPO 2017 World Congress in Dublin, which has been expertly captured in the short and snappy Congress Overview Video, which you can find on YouTube. Don't miss the very worthwhile cameos at the end!

    And while on the topic of must-see videos, make sure you've viewed the inspiring Welcome Address and thoroughly moving Keynote Speech by 47th Vice President of the United States Joseph R. Biden Jr. at the HUPO 2017 Leadership Gala in Dublin (both available on the HUPO home page).

    I would also like to take the opportunity to congratulate and welcome on board the newly elected HUPO Council Members, and of course HUPO  President-Elect Stephen Pennington.

    As promised, we have continued to evolve HUPOST over the course of 2017, which is now offered through an easily browsable overview so you can find your topics of interest even more quickly. I'm also very happy to announce that contributions from the various HUPO Initiatives will now be included in HUPOST as well, further broadening our content, and helping you to stay up-to-date with all that's happening in HUPO. And don't forget that you can always let us know at when youhave something to share, and that you can find us on social media: Facebook, Twitter, and LinkedIn.

    Finally, allow me to remind you that, if your HUPO membership is up for renewal, you can easily renew online through the HUPO website. Special rates apply for students and post-docs, while everyone else can take advantage of the discounted 3-year membership formula.

    Happy holidays and best wishes for the new year!

    Cheers, Lennart Martens 

  • 20 Nov 2017 5:42 AM | Anonymous

    Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

    A new initiative at HUPO2017 was a round table discussion with clinical scientist travel grant winners, the B/D-HPP executives, selected previous clinical scientist travel grant winners, and HUPO2018 organiser Ileana Cristea. The goal of the round table discussion is to gain insight on the challenging facing clinical scientists in proteomics research, and feedback how HUPO could facilitate their clinical proteomics research. In addition, it was hoped that each of the travel grant winners could work closely within one or more B/D-HPP initiatives.

    The five award winners hail from across the globe, with broad specialities.

    Dr Mariette Labots is a medical oncologist at the VU University Medical Centre, Amsterdam, The Netherlands. She is currently pursuing PhD in the OncoProteomics Laboratory led by Dr Connie Jimenez. Dr Labots has worked on phosphoproteomics of cancer tissues in response to targeted therapies.

    Dr J Robert O’Neill is a clinical lecturer and honorary specialty registrat in upper gastrointestinal surgery, University of Edinburgh, UK. After completing his PhD in 2014, which involved the use of proteomics to explore therapeutic target discovery, Dr O’Neill is currently building a program in esophageal cancer research in Edinburgh.

    Dr Emma Nimeus is a breast cancer surgeon at Skane’s University Hospital and principal investigator for the Breast Cancer Proteogenomics Group at Lund University in Sweden, in the next-door buildilng. Dr Nimeus has established an interdisciplinary and international collaboration to enable proteogenomics research using clinical samples procured from her clinical practice.

    Professor Richard D. Semba is an ophthalmologist from Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. He is one of the leaders of B/D-HPP EyeOME initiative which began in 2012. Prof Semba’s research aims to understand three important blinding eye diseases: age-related macular degeneration, chronic angle closure glaucoma, and idiopathic macular holes.

    Dr Krishna R Murthy is a vitreo-retinal surgeon and the medical director of Vittala International Institute of Ophthalmology, Bangalore, India. He recently defended his PhD from Amrita Vishwa Vidyapeetham. Dr Murthy’s areas of clinical interest include diabetic retinopathy, Retinopathy of prematurity, HIV related eye diseases and proteomics of the ocular structures.

    The round table began with self-introductions of research areas, how proteomics technologies are accessed, and any challenges currently facing the travel award winners. In-depth discussions between the participants explored diverse topics including the need for proteomic (and lipidomic) research, challenges to obtain access to advanced mass spectrometry technologies and to keep abreast of the fast pace of technology change.

    Finally, B/D-HPP executives and HUPO2018 organisers solicited and received feedback on how the HUPO World Congress program could be modified to further facilitate clinical proteomics research and collaboration. Look out for new ideas and formats at HUPO2018!

    From left to right: Hui Zhang (Cancer HPP co-chair), Mariette Labots (grant winner), Ferdinando Cerciello (past grant winner, B/D-HPP ECR rep), Robert O’Neill (grant winner), Emma Nimeus (grant winner), Jenny Van Eyk (B/D-HPP chair and executive committee member), Richard Semba (grant winner), David Herrington (past grant winner), Murthy Krishna (grant winner), Eric Deutsche (B/D-HPP executive committee member). Not pictured: Gil Omenn (B/D-HPP ex-officio), Fernando Corrales (B/D-HPP co-chair), Ileana Cristea (HUPO2018 organiser), Michelle Hill (B/D-HPP news article editor).

  • 23 Oct 2017 5:45 AM | Anonymous

    Nicki Packer, Macquarie University, Australia

    Protein glycosylation is a common and diverse modification crucial to the understanding of protein function in just about every biological system. Advances in mass spectrometry now allow hundreds and even thousands of unique intact glycopeptides to be identified from a single LC-MS/MS-based glycoproteomics experiment [1]. However, confident identification of intact glycopeptides is still challenging and correct spectral annotation remain heavily dependent on laborious manual expert interpretation of fragment mass spectra. Glycoproteomics is experiencing increasing attention these years not least within the HUPO community as demonstrated with a dedicated glycoproteomics sessions at HUPO2016. However, the described technical limitations are inhibiting new scientists from entering this exciting area of proteomics. Thus, there is a clear need for tools for accurate and confident automated glycopeptide identification.

    The past decade has seen promising developments of a range of MS-based software for intact glycopeptide identification [2]. To enable community evaluation of these developing tools, the new chair of the HGI, Prof Nicki Packer, Macquarie University, Sydney launched a new HGI study at HUPO2017. For this purpose, two large data files containing high resolution tandem mass spectral data of intact glycopeptides from human serum have been generated for this purpose by ThermoFisher. Combinations of dissociation modes (HCD, EThcD, ETciD and CID) were used to obtain the spectra. An expert panel will curate/analyse the data to create a consensus glycopeptide library, for comparison against the list of identifications being reported by participants in the study.

    We are calling for participants (of academic and/or industrial origin) that are either developers of glycoproteomics software and/or expert users (researchers) in glycoproteomics, to identify and report on the characterization of the intact serum glycopeptides using either their own software (developers) or by using one or more tools which they routinely use in their glycoproteomics research including manual interpretation (expert users). Participants are asked to report how they interpreted the data. We plan to send out the intact glycopeptide MS/MS data this year in order to present the preliminary results of the comparative study at the next HUPO in 2018, with a planned publication of the final results and conclusions to follow. Please contact if you would like to be part of this study.

    HGI Committee members:

    Prof Nicki Packer (Macquarie University and Griffith University, Australia) (Chair)

    Dr Morten Thaysen-Andersen, Macquarie University, Australia (Deputy Chair)

    A/Prof Daniel Kolarich, Griffith University, Australia (Deputy Chair)

    Dr Stuart Haslam, Imperial College, UK

    Prof Kai-Hooi Khoo, Academia Sinica, Taiwan

    Prof Goran Larson, Gothenburg University, Sweden

    Prof Katalin Medzihradszky, UCSF, USA

    Prof Giuseppe Palmisano, University of Sao Paulo, Brazil

    Prof Jong Shin Yoo, Korea Basic Science Institute, Korea

    Prof Joe Zaia, Boston University, USA


    [1] Thaysen-Andersen M, Packer NH, Schulz BL. Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease. Mol Cell Proteomics. 2016. 15(6):1773.

    [2] Hu H, Khatri K, Klein J, Leymarie N, Zaia J. A review of methods for interpretation of glycopeptide tandem mass spectral data. Glycoconj J. 2016. 33(3):285.

    Design of the new HGI study to compare the performance of current glycoproteomics software for N- and O-glycopeptide identification from high resolution MS/MS spectral data of a complex mixture of serum proteins.

Copyright 2016 - HUPO

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