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


  • 25 Jul 2017 3:11 PM | Anonymous

    Through the leadership of HUPO and Chromosome-centric HPP over the past several years, we now have a relatively complete ‘Parts List’ of the human proteome. The B/D-HPP initiatives spearheaded the characterization of tissue-specific proteomes in health and disease conditions, with most studies on adult-derived samples, and model organisations. The HPP-PediOme has a clear focus on the proteomic analyses of pediatric samples, including newborns, infants, young children and adolescents.  

    In addition to providing biomarkers for diagnosis of pediatric-specific conditions, pediatric proteome studies can also reveal early disease mechanisms for common adult conditions such as diabetes and obesity, thus contributing to prevention of disease. While proteomics analyses of pediatric samples present some obvious challenges, such as difficulty of sample collection and the limited sample volume compared to adult samples, the reduced number of potential confounding conditions may simplify the biomarker study design and analyses. 

    The human pediatric proteome (PediOme) project aims to co-ordinate an international effort to drive characterization of the human pediatric proteome in health and disease. Early efforts focussed on existing studies in pediatric proteomics, through a special Issue of Proteomics - Clinical Applications in December 2014, Focus on Proteomics in Paediatrics, and a review series in Clinical Proteomics from November 2015 to April 2016.

     

    The current co-chairs, Vera Ignjatovic (Murdoch Childrens Research Institute, Australia), Hanno Steen (Boston Children’s Hospital, USA) and Allen Everett (Johns Hopkins, USA) have developed a list of goals for the HPP-PediOme, including:

    • -       To create a worldwide pediatric biorepository network and inventory
    • -       To standardize the protocols for pediatric specific proteomic studies
    • -       To facilitate training, as well as collaboration between clinicians and scientist, thereby enable translation of outcomes.

     

    Ultimately, the PediOme Project aims to fully characterize the healthy pediatric proteome from birth until adulthood, and to utilize the knowledge of the pediatric proteome for the prevention of major adult diseases such as cardiovascular disease, diabetes and obesity. For more information and to participate, please visit HPP-PediOme, or contact one of the co-chairs. 


  • 05 Jun 2017 11:22 AM | Anonymous

    HUPOST: Where does your interest in quality control come from?

    DT: I’ve been in bioinformatics for twenty years now, and I have come to realize that black boxes harm users as well as bioinformaticists. I have therefore started to dedicate quite a bit of time to bioinformatics education. Many researchers in proteomics and metabolomics simply do not know the extent to which technical variation may be hiding biological variation in their experiments, so quality control represents a look inside the black box of these important methods.

    HUPOST: Can you tell us  a bit more about the HUPO PSI Quality Control Working Group?

    DT: The Quality Control Working Group (QC WG) is the first new Working Group of the HUPO Proteomics Standards Initiative in over a decade. It joins long-standing Working Groups such as the Mass Spectrometry and Proteomics Informatics Working Groups, which are responsible for mzML and MzIdentML/mzTab, respectively.

    DT: The QC WG is a group of researchers from proteomics and metabolomics that is dedicated to see quality control mature as a research discipline.  We must ensure that QC is accessible to people who may not be familiar with the intricacies of standard formats and statistical models. The focus of the QC WG, therefore, is on making quality control a part of everyday practice.

    HUPOST: Who should be interested in the Quality Control Working Group?

    DT: I strongly believe that quality control is of interest to everyone in the field. Just because something is not dramatic does not mean it’s non-essential. When I think about the ways in which our work can be useful, I think about a principal investigator writing a solid research proposal, about a core facility director who wants to deliver top-notch service, and about a technician besieged by people who want their data “yesterday.” All of them need quality control, and we hope to arm these people with useful tools. The focus is currently on quality control for mass spectrometry, but the scope within this field is very broad, and includes both proteomics and metabolomics applications.

    HUPOST: What are the desired outcomes of the work of the Quality Control Working Group?

    DT: The primary target in our sights is interoperability; if a researcher creates a new set of quality control metrics, we want the output of the tool that calculates these metrics to be compatible with a statistical tool that was originally built to analyze another set of QC metrics. The qcML standard format for quality control metrics is at the core of this endeavour. To put it another way, quality control information is the commodity that we want to trade among metric generation software, statistical frameworks and repositories, with qcML as the coinage.

    DT: Practically, this will require tools that generate metrics (for instance, QuaMeter and OpenMS) to produce qcML as output on the one hand, and statistical frameworks that can read and digest qcML on the other hand.

    DT: Moreover, the objective of these statistical models should be to make tangible decisions based on these data, such as flagging an experiment as an outlier. Here, reliability is key. If a given tool repeatedly informs a technician that something is out of whack, the tech will quickly learn to ignore it if there are too many false positives.

    DT: And of course, we endeavour to lower thresholds for adoption of quality control in everyday practice; the less effort required to emplace quality control regimen, the more likely people are to put it into use.

    HUPOST: What would you say to prospective participants in the Quality Control Working Group to raise their interest?

    DT: First and foremost, like all PSI Working Groups, the QC WG is always open to participation! The group consists of people who are very invested in quality control, who frequently bounce ideas off each other.

    DT: But more than this, the QC WG really does need your insights; not only to learn what users require, but also your insights into statistics to harvest conclusions and decisions from quality control data. We also need the input from vendors; ideally their instrument control software would produce qcML directly to support assessment of these workflows, and vendors have great insights into the workflows that are right around the corner for our field!

    DT:If you’re interested in participating, there’s a monthly Google Hangouts call, a QC WG GitHub repository, and a mailing list. Of course, the QC WG’s web page is also a good place to start.

    HUPOST: What is the Quality Control Working Group working on right now?

    DT: When qcML was first published, it was built around the available knowledge at the time. We are now extending qcML to accommodate a broader range of experiment types (such as selected reaction monitoring and data-independent acquisition). To achieve this, we need to address two challenges: how do we broaden the scope of qcML into new types of experiments, and how prescriptive should the QC WG be with regards to the description of quality control metrics? At our most recent meeting in Beijing in April, we came to the conclusion that a developer needs to have access to concise reading materials that allows them to create a valid and useful qcML quickly. It should not be necessary to understand the HUPO PSI working method and development process to be able to write a functional qcML file.

    DT: Both of these challenges again boil down to lowering thresholds to adoption: making sure that quality control can easily be applied to your experiments, regardless of their type, and enabling developers to quickly and easily adopt qcML in their software.

    HUPOST: Does the Quality Control Working Group have a presence at the 2017 HUPO Conference in Dublin?

    DT: Of course! There will be an overall PSI session at the conference, and we are always well represented in the Bioinformatics Hub as well.

    HUPOST: Thank you very much, and we wish the Quality Control Working Group a bright future!

  • 05 Jun 2017 11:15 AM | Anonymous member (Administrator)

    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

    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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