NewS

The neXtProt peptide uniqueness checker maps uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants. The use of this tool is recommended in the latest HPP guidelines as it can be used to define which peptides can be used to validate the existence of human proteins. The tool is described in the recently published Bioinformatics Application Note https://doi.org/10.1093/bioinformatics/btx318.

The 6th newsletter of the Chromosome-centric Human Proteome Project is now available online, read it here. 

In this issue:

• Editorial
• C-HPP Leadership Update
• C-HPP Principal PIC
• A Brief Introduction Of New PIs and Plans
• JPR SI Call For Papers
• Working Group Formation of C-HPP
• Briefings in the 2016 C-HPP Workshops 
• Future C-HPP Workshops

The hPOP (Human Personalized Omics Profiling) project is designed to study the variance of molecular markers across a large number of participants. Recent advances in high throughput technologies allow profiling of thousands of analytes within a single experiment. These measurements could potentially be used to diagnose disease early, monitor treatment progression and stratify patient groups to ensure each individual obtains the treatment best suited to their needs. This personalized approach to medicine would include continuous monitoring of thousands of parameters over a whole lifetime. However, in order to be able to interpret such data, we need to have a better understanding of the underlying natural variation of these molecular parameters in health and disease. Only if we know the natural ranges of individual analytes, the expected responses to perturbations and the long-term trends in their levels, can we draw meaningful conclusions from comprehensive personalized profiling.

In this project, we aim to use a multi-omics approach to study the genome, epigenome, transcriptome, proteome and metabolome of a large number of healthy volunteers. The hPOP project will be launched officially at the 2016 HUPO in Taipei where samples from several hundred people will be collected. The current protocol includes sampling of blood, urine and stool after overnight fasting. Additionally, a detailed questionnaire about food habits, personal health, physical activity and stress levels will be filled out by each participant. All data will be made available to the scientific community under public domain which will allow multiple research groups to use the generated data in their own studies and perform their own analysis of the data.

To find out more or to join the hPOP mailing list, visit the website. 

Proteogenomics, integration of proteomics, genomics, and transcriptomics, is an emerging approach that promises to advance basic, translational and clinical research.  By combining genomic and proteomic information, leading scientists are gaining new insights due to a more complete and unified understanding of complex biological processes.

Advanced bioinformatics approaches are needed to entirely use the complete information spectra acquired in genomics, transcriptomics and proteomics studies.  A DREAM Challenge offers a chance to crowdsource the analysis of numerous rich data sets at once (one of the largest public repositories of proteogenomic sequence data) and thereby compare aspects of various methods to better understand biological features that drive early cancer progression.

To this regard, the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, in partnership with DREAM Challenges, announce the NCI-CPTAC DREAM Proteogenomics Challenge (estimated launch date is mid-June).  The aim of the challenge is to encourage the generation of computational methods for extracting information from the cancer proteome and for linking those data to genomic and transcriptomic information. The goal is to predict proteomic and phosphoproteomic data from multiple other data types.  Method performance will be blindly evaluated using a previously unseen validation dataset generated by CPTAC.

DREAM Challenge will be run in the Google Cloud, and provide a prize award sponsored by the NVIDIA Foundation.  Nature Methods also supports the submission of an overview paper of the Challenge, contingent on a standard evaluation process.

For Registration, click here

Please visit the DREAM website for further details on DREAM challenges, including history, previous challenges and FAQs.

Dear HUPO colleagues,

The HPP is reaching out to clinical scientists or clinicians who are using or consider using proteomics for their research projects. HPP is supporting six (6) clinical scientists with a travel grant to attend the 2017 HUPO World Congress in Dublin, Ireland that will take place from September 17-21, 2017.

Travel grant recipients will receive USD $1,000 to offset travel and hotel costs in addition to complimentary congress registration. The recipients are expected to actively participate in the HUPO congress, particularly in the activities and discussions related to the HPP. Further information on the HUPO 2017 congress and HPP activities in Dublin can be found at http://hupo2017.ie/.

Application deadline: Friday, June 30, 2017

For more information and application instructions visit https://hupo.org/HPP-Clinical-Scientist-Travel-Grants.

Congratulations to the HUPO2016 Taipei PhD abstract competition winners!

Christopher Ashwood (Macquarie University, Australia)

At HUPO, I saw innovative techniques that I had not been exposed to before this conference. I felt inspired by watching a great range of presentations by world-renowned experts in their area of expertise and particularly enjoyed the sessions on glycoproteomics. During breaks between sessions, I was exposed to a huge range of posters from researchers all around the world.

Thanks to the mentoring pre-conference workshop, I learned about the current challenges and expectations in academia. My PhD experience has also been improved by learning about the best current practices in the field of proteomics. Due to this conference, I’ve been able to be up to date on the most recent advances in instrumentation as well as using existing technology to address well-known challenges. The most important point I took away from this conference was the importance of bioinformatics in processing big data sets for more effective biological studies.

During my attendance of HUPO 2016, I felt encouraged that my research area is important to HUPO and thankful for the organising committee for setting up this conference.

Margherita Dell´Aica (ISAS, Germany)

Last year I had the unique experience to attend the HUPO World Congress in Taipei. The program was packed with exciting talks covering cutting edge research, e.g. Technological Advancements, PTMs, Computational Omics and Cancer Research, rendering it the ideal opportunity to promote my own work. The key-note lectures provided deeper (historical) insights and I enjoyed listening to top speakers I only knew from articles.

I am very pleased that I became one of three winners of the HUPO PhD abstract competition. Getting more actively involved into this super-international community and the great experience to promote and defend my work in front of leaders in the fields truly were inspiring and motivating.

The Conference atmosphere was remarkable, such as the kindness of the Taiwanese, the food, the beauty of Taipei’s cosmopolitan streets and the relaxing view of Sun Moon Lake.

Altogether, participating the HUPO 2016 provided me high professional feedback, novel ideas to improve my work, to collaborate with other scientists, and to further pursuit my scientific goals and career. I will definitely participate again in coming years.

Zhiduan Su (University of Sydney, Australia)

It is my great honour to attend 15th HUPO congress in Taipei, which is also an unforgettable experience to me. I also need to thank HUPO 2016 Committee to give me an opportunity to present my study in this congress. My project is about redox proteomics and cysteine oxidations and so far focused on metabolism-disordered cell models. It was really a fantastic and precious occasion that almost all "redox proteomics stuff" could get together and exchange opinions with each other during the congress that might contribute to better understanding of our studies. Also, I was able to meet a few "big guys" and listened to what they were doing recently and what they wanted to do next, which were relevant to the present and future of proteomics progress. Certainly, meetings with old friends during the conference were the memorable moments in my life as well.

HUPO 2017 Abstract Extension

Abstract submissions to the 16th Human Proteome Organization World Congress have been extended to 3 May 2017. Read more >

ECR Manuscript Competition 

The Early Career Researcher (ECR) Initiative of the Human Proteome Organization is pleased to announce the 3rd ECR Manuscript Competition to take place at HUPO 2017 in Dublin! Deadline 5 June 2017. Read more > 

PhD Abstract Competition

Once again, HUPO is holding a PhD Abstract Competition. 8 abstracts will be selected based on excellence to have a short oral presentation at HUPO 2017 in Dublin. Deadline 3 May 2017. Read more >

HUPO Elections

HUPO is seeking candidates to serve on the HUPO Council for three-year terms beginning January 2018 (2018-2020). We invite you to nominate yourself and other scientists from your region. Deadline 30 April 2017. Read more >

Editor's Note

Welcome to the new HUPOST! As Emma Lundberg, our much-appreciated outgoing Editor, announced in the previous HUPOST, we updated the format for 2017. Key points are now included in the email, and our circulation has broadened to reach an even wider audience. HUPOST’s frequency has also increased to every two months, alternating between a short and snappy overview of current news, and an extended version that covers interesting developments in the field of proteomics.

Speaking of interesting developments, allow me to remind you that the HUPO 2017 World Congress in Dublin on 17-21 September is now only 5 months away! Abstract submissions will now be accepted until 3 May, so you can still join us and share your latest work. I very much look forward to hearing about it, and to meeting you, on the Emerald Isle in September!

Meanwhile, enjoy the new HUPOST, and make sure to let us know at office@hupo.org when you have something to share! As always, you can find us on social media: Facebook, Twitter, and LinkedIn.

Cheers, Lennart Martens - HUPOST Editor

President's Message

There has never been a more exciting time for proteomics. We can rapidly measure thousands of molecules and posttranslational modifications, and there are large initiatives such as the Cancer Moonshot and Gene-Tissue Expression Project in which proteomics will make an important contribution. As technological advances continue proteomics will play an increasing role in large-scale influential projects.

A valuable part of all of these efforts is the Human Proteome Project (HPP; 1) which aims to map the proteome parts lists: protein coding genes, splice and allelic isoforms. It also aims to advance the proteomics of a wide range of human biology and disease, for example, cardiovascular disease, diabetes, cancer. With respect to the latter, we are assembling a list of popular proteins for each major human disease (2).

The HUPOST is HUPO’s forum for disseminating advances in our field. We hope to keep the community abreast of the latest advances and technologies.

Cheers, Mike Snyder - HUPO President

1) Advances of the HUPO Human Proteome Project with broad applications for life sciences research. Omenn GS. Expert Rev Proteomics. 2017 Feb;14(2):109-111. doi: 10.1080/14789450.2017.1270763. Epub 2016 Dec 22. No abstract available. PMID: 27935328

2) Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. Lam MP, Venkatraman V, Xing Y, Lau E, Cao Q, Ng DC, Su AI, Ge J, Van Eyk JE, Ping P. J Proteome Res. 2016 Nov 4;15(11):4126-4134. Epub 2016 Jul 19. PMID: 27356587

Dear HUPO Members,

I am seeking candidates to serve on the HUPO Council for a three-year term that will begin January 2018 (2018-2020).

Each Councilor must be a current HUPO member who is a scientist from the public or private sector with at least ten (10) years of professional experience in educational, research or commercial activities related to the purposes of HUPO. We invite you to nominate yourself or other scientists from your region - Central region (Europe/Africa), Eastern region (Asia/Oceania), and Western region (Pan-America). Please check with your nominee to be sure they are willing to stand for election.

To nominate a colleague or yourself please complete the 2017 Elections Nomination Form (available here) and submit it to office@hupo.org before 30 April 2017.

If you nominate a colleague please note they will be asked to confirm their willingness to stand for election. The current council list can be found here.  

Thank you for your support,

Henning Hermjakob

Chair, HUPO Nominations and Election Committee

• 2017 HUPO Council Nomination Form
  
• Deadline to receive nominations: 30 April 2017

Dear HUPO Members,

The Human Proteome Organization is pleased to the announce the HUPO-endorsed Cardiovascular Initiative Workshop. The workshop features outstanding scientists from across the HUPO/HPP community. View the programme online.

The workshop takes place on 2 April 2017, during the Proteomic Forum in Potsdam, Germany. For more information, and to register, visit http://www.proteomic-forum.de/ or contact dgpf@conventus.de.

Best wishes, 

Christoph Borchers

Chair, HUPO Marketing Committee

      

The Human Proteome Organization presents awards annually at the World Congress. The HUPO 2017 World Congress is in Dublin from September 17-21. Award recipients will present a brief talk during the Congress award ceremony. These distinguished awards recognize the outstanding efforts of individuals (or groups) advancing the field of proteomics. Nominations are done through an online submission form and no supporting documents or attachments are required.

You are invited to nominate award candidates! 

Nomination Deadline: April 17, 2017 

Nomination Requirements

HUPO is now accepting nominations for the following awards:

Distinguished Achievement in Proteomic Sciences Award ($3000, sponsored by Journal of Proteome Research - ACS Publications) recognizes a scientist for distinguished scientific achievements in the field of proteomic science. 

Discovery in Proteomic Sciences Award ($3000, sponsored by Journal of Proteomics - Elsevier BV) recognizes a scientist for a single discovery in the field of proteomics. 

Science and Technology Award ($3000, sponsored by the HUPO Industrial Advisory Board) recognizes an individual, or team (of up to three people) in private industry who played a key role in commercialization of a proteomics technology, product or procedure. The emphasis for the award is on making the technology, product or procedure widely available, which is different from the basic scientific invention. 

Clinical and Translational Proteomics Award ($3000, sponsored by Clinical Proteomics - BioMedCentral) recognizes a scientist for distinguished scientific achievements in the field of clinical and translational proteomics. 

Distinguished Service Award ($3000, sponsored by HUPO) recognizes an exemplary member of the proteomic research community whose dedicated service has made indispensable contributions to the organization and mission of HUPO.