HUPO Connect 2020

Celebration of 90% completion of the Human Proteome

• Special issue of the Journal of Proteome Research selecting 60 Human Proteome Project related papers over the past 10 years is available online here.
• Editorial of Chris Overall on "The HUPO High-Stringency Inventory of Humanity’s Shared Human Proteome Revealed" is available in pdf format here.
• The metric paper showing completion of >90% of the Human Proteome in the Journal of Proteome Research is available in pdf format here.
• Paper entitled "A high-stringency blueprint of the human proteome" in Nature Communication is available in pdf format here.

Agenda of C-HPP PIC Virtual Meeting Monday October 19, 2020

Meeting Start 2:15 PM PST

1. Roll call
2. Virtual format notes
3. Acceptance of the agenda
4. C-HPP Update 2020
   • Russian Workshop 2020
   • Busan Workshop 2021
   • neXt-MP50
   • neXt-CP50 given by Young-Ki Paik
   • JPR SI 2020
   • Virtual Issue on HPP Decade 2020
5. Elections
   • Results: HPP Chair 2020-2021
   • Upcoming: HPP Co-Chair 2021-2022 nominations requested
   • C-HPP Co-Chair 2021-2023: Election for Co-Chair, Dr Lydie Lane.
   • Nominations from the floor
6. Future of neXt-Prot (Lydie Lane and Chris Overall)
7. Chromosome leadership Chr 21/22
8. Next PIC meeting @ 24^th C-HPP Workshop
   • Busan Korea, June 28, 2021
9. Open Discussion
10. 3:00 PM PST Meeting Closure

PIC meeting minutes is available in pdf format here.

Remarks:

• Last Year (2019) Report: For the neXt-MP50 challenge, considerable evidence was found for MPs, but failed to satisfy the HPP Guidelines 3.0 and so remain as candidate ‘found’ MPs. 
• For the neXt-CP50 challenge, although 14 teams are currently working on the uPE1 Dark Proteins there was no net decrease in the current 1,254 uPE1 proteins during the past year.

Highlights from last PIC meeting (Adelaide 2019)

• Discussing to target PE1 proteins, which does not have evidence using mass spectrometry-based methods (non-MS PE1).
• Different definitions of non-MS PE1: identical sequences (not possible to distinguish by MS), high sequence homology, low abundant (olfactory receptors, GPCRs), no tryptic peptides of proteins.
• Include more technologies for Missing Proteins (MPs): immunocapture, top-down, PTM enrichment, protease cleavage products etc.
• 5 MPs per each B/D-HPP groups specific to their analyzed tissues/cell lines (100 MPs).
• Example for non-MS PE1 is prestin is an example of proteins without MS but strong other evidence. To provide MS evidence for non-MS PE1, we should get the top 10 protein with strong non-MS evidence (e.g. use of MissingProteinPedia) and concentrate to find MS evidence for those.
• to identify other methods for MPs identification: Journal Proteomics Research paper on the history of MPs of Chr17 identification e.g. protein/protein interaction datasets or in unique samples and how to analyze the remaining ones.
• new approach to identify MPS and uPE1 is by activation of passive (dormant) pathways/cycles to express MPs. Functional annotation of uPE1 using I-TASSER/COFACTOR and combine this with tissue/condition prediction.

The Chromosome Centric Human Proteome Project (C-HPP) Annual Report 2019-2020 prepared for the 2020 HUPO Council

The report of chromosome teams on neXt-MP50 in 2019-2020 is available in pdf format here. September 3, 2020.

HPP Day, October 22 

16:15 - 17:45 UTC, HPP Session 1 - HPP Initiative/Pillar Planning
Chairs: Robert Moritz, United States, Sue Weintraub, United States

• Relevance and Future Projections of Proteomics in the Pharmaceutical Industry, Jennie Lil, United States
• Translating Proteomics to the Clinical Arena, Michael Roehrl, United States
• Target 2035 - Pharmacological Modulators for All Human Proteins, Cheryl Arrowsmith, Canada
• Expanding Proteomics Beyond the Proteomic Community, Jochen Schwenk, Sweden
• Bringing context to substance, Relevance of the Human Proteome Project, Robert Moritz, United States
• Review and Updates (Future Planning/Developments)
  • C-HPP, Chris Overall, United States
  • B/D-HPP, Ileana Cristea, United States
  • Initiatives and 4 Resource Pillars, Cecilia Lindskog, Sweden, Eric Deutsch, United States, Lydie Lane, Switzerland, Ed Nice, Australia, Michael Roehrl, United States and Susan Weintraub, United States
• Written Questions from the Floor

18:00 - 19:30 UTC, HPP Session 2 - Moving the HPP Towards Proteome Functionality
Chairs: Ruedi Aebersold, Switzerland, Rebekah Gundry, United States

• Background and Outline, Ruedi Aebersold, Switzerland
• SAB Session with 3 Break-Out Groups, All
  • Breakout I. How can proteomics make the link from measuring molecules (proteins) to biological function? Rapporteur:Juri Rappsilber, Germany
  • Breakout II. HPP can claim that the discovery of exemplary proteins from almost all human loci can be confidently detected and routinely measured. How does HPP build on that to advance life science and clinical research? In other words, how can we explore ( e.g. within HPP) the full extent of the complexities of the proteome and how can this be translated into new biology? Rapporteur: Kathryn Lilley, UK
  • Breakout III. What are the bottlenecks to increase the uptake and dissemination of proteomics? Rapporteur: Cathy Costello, United States
• Summary Reports to Combined Group, All

19:45 - 21:15 UTC, HPP Session 3 - HPP International Outreach Exploration
Chairs: Cecilia Lindskog, Sweden, Ed Nice, Australia

• Human Cell Atlas/Chan Zuckerberg Foundation/International Opportunities, Emma Lundberg, Sweden, Neil Kelleher, United States
• International HUPO External Development Initiative Panel, Sudhir Srivastava, United States, Sanjeeva Srivastava, India,
• Kristin E Burnum-Johnson, United States, Eleftherios Diamandis, Canada, Anthony Whetton, United Kingdom
• USA and Cancer Moonshot Opportunities, Mike Snyder, United States, Henry Rodriguez, United States
• Other Opportunities from the Floor
• Incoming HUPO Presidential Address to the HPP, Yu-Ju Chen, Taiwan