Péter Horvatovich, University of Groningen, The Netherlands
With a good attendance at the Thursday HPP workshop, talks on the Knowledge Base Pillar progress and outlook were well presented by Eric Deutsch, Lydie Lane and Henning Hermjakob. They highlighted the raw MS data exchange between ProteomeXchange and partners such as Pride, iProx, JPOST, MassIVE and Panorama, which serves to collect all public proteomics data generated by the scientific community, protein evidence status in PeptideAtlas and neXtProt according to the latest release. The report also gave updates on the peptide uniqueness checker and introduction of Universal Peptide Identifier that aims to identify specific MS/MS spectra in a ProteomeXchange dataset.
Measurement of intact proteoforms with top-down approach to map the proteome of human cell types (a Cell-Based Human Proteome Project) was presented by Neil Kelleher. In discussions with the Chairs of the C-HPP a collaboration has been formalised to prepare a proposal for the C-HPP and HPP ECs titled “The Human Cell Proteome Atlas”. This is an extension of the current rare cells and tissues project of the C-HPP led by Chris Overall. In the HCPA the current bottom up rare cells and tissues proteomics projects of the C-HPP would be complemented by the a top-down proteomics approach led by Neil to produce an atlas of proteins and proteoforms making up each of the hundreds of different cells of the human being.
On emerging technology topics, Bonghee Lee (Korea) presented CRISP/cas9 technology used to modify human iPSC and differentiated cells for Hemophilia B treatment . Janne Lethiö (Sweden) presented proteogenomics pipeline that can be used to process high-resolution iso-electric focusing fractioned peptides to better annotate protein coding region of the human genome and identify variants in human blood. Mike Snyder presented ‘Grand Challenges for the Entire Field of Proteomics’ where he addressed an outlook and plans on the directions of the proteomics technology development and those key issues that the HPP will address in the future. Henry Rodrigez showed an overview on the international collaboration within Cancer Human Proteome Project and within the Cancer Moonshot international collaboration. Mark Baker, incoming HPP Chair (Australia) outlined his strategic plans on the key HPP components, C-HPP and B/D-HPP in the next 2 years. The Antibody Validation Initiative showed their progress to develop validated antibody reagents for the scientific community. The September/October neXt-MP50 report from the Chromosome Teams was presented to the HUPO council. The chromosome teams reported the identification of ~401 missing proteins identified according to the C-HPP guidelines in 2018. These were presented in 26 J Proteome Res Special Issue papers in December 2017 and will be reported in 34 J Proteome Res papers in the upcoming December 2018 Special Issue. In addition, the Chromosome Teams reported HPP findings in 63 other papers in 2018, many of which reported missing proteins or uPE1 functionalization. At the end of the first quarter 2019 the next builds of the Peptide Atlas and NeXtProt will have parsed through these and other Proteome Exchange data sets for confirmation of found MPs.
The C-HPP welcomes the leadership of Dr. Rob Moritz, Institute of Systems Biology, Seattle, WA as the new leader of the Chromosome 6 Team, that has passed from Christoph Borchers, University of Victoria. The experimentalists, coders and data-base curators at ISB are a welcome addition to the C-HPP and join active labs at the University of British Columba, Vancouver, in a “Cascadia Chromosome Collaboration”.
Plans are moving forward for the 21st C-HPP Project Symposium, to be held May 12-14, 2019 in Saint Malo, France. Focussing on “Illuminating the Dark Proteome” the symposium will be an important milestone for the uPE1 project and will include speakers from the B/D-HPP on functionalizing the dark proteome. What is also certain, the cuisine at this meeting will not be dark or need illumination thanks to Charles Pineau, Chair of the workshop.