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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.


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  • 05 Jun 2017 11:15 AM | Deleted user

    1. Human Brain Proteome Project (HBPP)

    Garcez et al. Sci Rep. 2017 Jan 23;7:40780. doi:10.1038/srep40780. Zika virus disrupts molecular fingerprinting of human neurospheres.

    Combining proteomics and mRNA transcriptional profiling, we found over 500 proteins and genes associated with the ZIKV infection in neurospheres associated to impairments in the cell cycle and neuronal differentiation. Our results point to biological mechanisms implicated in brain malformations, which could be exploited as therapeutic potential targets to mitigate it.

    2. Human Immuno-Peptidome Project (HIPP)

    Abelin JG, Keskin DB, Sarkizova S, Hartigan CR, Zhang W, Sidney J, Stevens J, Lane W, Zhang GL, Eisenhaure TM, Clauser KR, Hacohen N, Rooney MS, Carr SA, Wu CJ. (2017). Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity 46:315-326.

    HLA class I binding prediction has traditionally been based on biochemical binding experiments. Abelin and colleagues present an LC-MS/MS workflow and analytical framework that greatly accelerates gains in prediction performance. Key advances include the discovery of sequence motifs and improved quantification of the roles of gene expression and proteasomal processing. 

    Workshop Report from 8th Workshop on Affinity Proteomics, Jochen Schwenk

    The 8th Workshop on Affinity Proteomics was held in Alpbach, Austria from March 12th-15th. The meeting brought together more than 130 attendants and recent advances in the generation and use of binding reagents. A broad range of applications were presented including expanded use of microarray and immunoassay systems, as well as mass spectrometry based assessment of antibody selectivity. A panel of researchers, reagent providers and journal editors then discussed the challenges and opportunities of the field today and how to address these for the years to come. 

    This included the need to: 

    • validate the affinity reagent in and for a specific application and sample context
    • provide transparent information about validation (e.g. accessibility to primary data)
    • collect trackable information about affinity reagent (e.g. origin, LOT and product number, clone or sequence)
    • standardise the assessment criteria and assays

    The 9th Workshop on Affinity Proteomics is planned to be held in Alpbach in two years.

    Upcoming Workshops:

  • 05 Jun 2017 11:03 AM | Anonymous member (Administrator)

    The HUPO 2017 Conference in Dublin is host to several pre-conference workshops and events on Sunday 17 September, one of which is a repeat of the acclaimed Mentoring Day (you can find a report on last year’s Mentoring Day in the B/D-HPP Newsletter). We were eager to find out more about this event, and we therefore spoke with representatives from the three organizing groups:

     HUPOST: Can you tell us something about the group you represent, and about the link between the group and the Mentoring Day?

    MD: YPIC was founded by EuPA to represent young investigators in proteomics, and to address their specific needs. We surveyed these needs, and we found that the responses meshed very well with what he Mentoring Days at previous HUPO Conferences (Vancouver 2015, and Taipei 2016) was covering. As a result, we contacted HUPO’s ECR to join them in organizing the Mentoring Day at HUPO 2017 in Dublin.

    JFB: The HUPO ECR was founded at HUPO 2015 in Vancouver, under the auspices of the Biology/Disease Human Proteome Project Excecutive Committee. The goal of the HUPO ECR Initiative is to transmit the HUPO ideals to the next generation of proteomics leaders. And mentoring represents one of the strongest links between generations of researchers. The Mentoring Day was therefore conceived as a combination of lectures and brainstorming sessions to provide young scientists with concrete examples and tips on how to build a career in proteomics.

    VS: EuBIC is a group of young researchers that are active in the field of computational proteomics. This group is very much focused on the needs of proteomics researchers, and therefore aims to provide educational materials and workshops to bring the bioinformatics and proteomics communities closer together. For the Mentoring Day, EuBIC especially wants to help young proteomics researchers in handling their bioinformatics, which can quickly become an important issue in the ever more complex experiments performed today.

    HUPOST: What exactly can participants expect from the Mentoring Day?

    JFB: The Mentoring Day physically brings established proteomics experts and early-career proteomics researchers together in a friendly and informal atmosphere. Young researchers can learn from their shared experiences, ask questions, get advice, and present themselves. The Mentoring Day is very interactive, and consists of sessions aimed at personal and career development opportunities, through panel discussions with industry, brainstorm sessions, and games. A few comprehensive and dynamic talks are added to this exciting mix for inspiration and discussion points. Of course, attendees are encouraged to share their own perspective and to join the debate, all in a friendly and constructive atmosphere.

    MD: At the Mentoring Day, young and established scientists mix in an informal atmosphere. We’ll be discussing the relative merits of careers in industry and academia, the importance of networking and the ways to go about creating such networks, as well as the intricacies of the publication process. The final round table will be an open brainstorm on the future of science, and the role of proteomics in that future.

    VS: The Mentoring Day will also have a special session dedicated to finding answers to bioinformatics problems, and to discuss open data in proteomics.

    HUPOST: Who should join the Mentoring Day?

    JFB: Young researchers without age, experience, or culture limitations. We are trying to cover the needs from Master’s students to young PIs that are starting their own labs.  Our mentors will be sharing their professional knowledge, but also personal advice on, for instance, maintaining a healthy work/life balance.

    MD: The Mentoring Day is open to all interested attendees of HUPO 2017, as there is bound to be something interesting for everyone, regardless of their actual career stage.

    JFB: Exactly! Established researchers and leaders in the field can for instance come to be inspired by the fresh enthusiasm of the young researchers, and can take the opportunity to meet their future students, postdocs or collaborators.

    HUPOST: What are your desired outcomes for the Mentoring Day?

    MD: An ideal outcome for me would be a lively social event at the end of the day, where groups of young and established researchers mix and discuss the topics brought forward during the day, and any other topics they find interesting.

    VS: And through this, we will hopefully be able to boost the confidence of young researchers in taking control of their own career, which includes a deep understanding of the publishing process from the points of view of an author, an editor, and a reviewer. Especially the latter is a complex task that is easily misinterpreted as a call for harsh criticism rather than as a constructive process to help peers perform even better science.

    MD: Precisely! And young researchers can moreover be overwhelmed by the impressive keynote presentations given by well-established researchers at a Conference such as HUPO. It is therefore very important to show them how these established researchers also struggle to produce these wonderful results, and that science can be complicated for everyone.

    JFB: For me, the Mentoring Day should allow early-career proteomics researchers to gain more visibility within the proteomics community, to polish their communication skills, and to learn from someone else's mistakes. Meanwhile, established experts will be able to realize that the times, needs, and opportunities for young researchers have changed.

    HUPOST: What would you say to a prospective participant to convince them to attend the Mentoring Day?

    VS: You know all those questions about science, your career, and your future that you were always afraid to ask? We’ll be discussing and answering these during the Mentoring Day!

    JFB: Come and speak face to face with experts from academia, industry, and bioinformatics. And importantly, we always have sweets available and will hopefully conclude with a lively happy hour after the last session!

    MD: If you do not already know what you will do after your PhD or postdoc, the Mentoring Day will provide you with the information you need to answer that question.

    HUPOST: Do you have any other initiatives ongoing or planned that we should know about?

    JFB: An important currently ongoing ECR activity is the ECR Manuscript Competition. Here, early-career researchers compete with their colleagues from all over the world for their work to be selected among the three best proteomics manuscripts of the year. This competition provides an opportunity to highlight your work, and to present yourself to an international audience. The award(s) will be announced at the HUPO 2017 closing ceremony and the three finalists will receive a monetary price ($1,000 USD for first place, and $500 USD for two runner-ups). Be quick, though, as the application deadline is 5 June 2017! Find out more at: ECR Manuscript  

    MD: YPIC is currently hosting its YPIC Challenge, where participants get mailed a vial with nineteen peptides, which construct a sentence from a book. The challenge is to obtain the sentence, and identify its source. Participants write a small manuscript to describe their efforts, and the best submission wins a EuPA Travel Scholarship, which can be used to attend any EuPA or HUPO conference in the future. While the challenge may sound easy, it is not. For one thing, turning the Oxford Dictionary into a sequence database will not work, and this is therefore de facto a de novo assignment. Oh, and even if you do not have a mass spectrometer available, at least one of the acquired data sets will be shared soon, thus allowing bioinformaticians to start working on the problem as well! Find out more about the YPIC challenge at: YPIC Challenge registration 

    MD: At the HUPO 2017 Conference, YPIC is also organizing Meet the Expert Sessions on Monday 18, Tuesday 19, and Wednesday 20 of June during morning coffee break. Registration will be necessary, and questions are to be pooled in advance. A mailing about these sessions will go out to all registered HUPO 2017 Participants in the next weeks!

    VS: EuBIC will be participating in, and contributing several workshops to, the HUPO 2017 Bioinformatics Hub. EuBIC and YPIC are also planning to launch an Online Proteomics Job Fair for proteomics and proteomics bioinformatics at HUPO 2017, to be hosted on the web site of EuBIC and the EuPA Educational Committee: Proteomics Academy 

    HUPOST: Thank you all very much, and we wish you a sparkling Mentoring Day!

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