C-HPP PIC meeting at HUPO Connect
HUPO Connect 2020 will be held between October 19 and 22 and C-HPP PIC meeting is planned on Monday, October 19, 17:15 EST time. The topics to be discussed will be
- report and progress of chromosome teams in next-MP50 and next-CP50 projects.
- filling the open team positions for Chromosome 21 and 22.
- discussion of boosting joint chromosome team activities and collaboration with teams in B/D-HPP.
- Discussion of future C-HPP directions.
- The future of neXt-Prot. How to prevent this essential HUPO knowledge base from shuttering due to lack of funds
We ask all chromosome teams to update their results and potential team changes on C-HPP Wiki until HUPO Connect 2020.
Highlights from the C-HPP neXt-MP50 chromosome team reports:
- An issue arising from analysis of the team reports is that a large number of missing proteins that were reported “found” and discussed in their papers were either not captured by Peptide Atlas for analysis or failed reanalysis by Peptide Atlas and so were not promoted PE1 status
- Considerable evidence was found for MPs, but failed to satisfy the HPP Guidelines 3.0 and so remain as candidate ‘found’ MPs.
- Recommendation: Information regarding these candidate MPs should not be lost but compiled (to be determined where, how and format) so as to be accessible to guide and inform ongoing and future proteomics studies by the community, directed data analysis of similar tissue/cells in Proteome Exchange and current literature to generate evidence sufficient to meet the HPP Guidelines.
- Several chromosome teams (e.g. Chr 5, 12, 15) are active in the Cancer Moonshot and CPTAC projects and successfully analysing this data for MPs.
- Chromosome 6 initiated a directed search for PE1 proteins lacking MS evidence (termed non-MS PE1 proteins), with several identified by MS (in human bone) that met the HPP Guidelines for PE1 identification by MS.
- A precision medicine molecular corrector drug was developed by Chr6 team members that was shown to restore functional levels of a mutant protein isoform of MALT1. Untreated, this mutant protein led to a rare immunodeficiency disease. The disease was phenotyped in a previous paper by proteomics and TAILS N-terminomics that led to this discovery and then drug candidate.
- Chromosome 10 has assembled a comprehensive and one of the world’s largest collections of full-length Gateway plasmids representing 90% of all human protein-coding genes and are distributing the collection through their repository and distribution web portal DNASU (dnasu.org). Currently, Chr10 has full-length plasmids for 175 of 804 missing proteins, which are available to the entire C-HPP team. Chr10 (with Chr 5, 15, 16, and 19), have been providing the IVTT-compatible plasmids for missing proteins to other members for IVTT-assisted SRM and continue to generate more plasmids.
- The Chromosome 12 (South and SE Asia) team has recruited Radislaw Sobota, Singapore as a new member of the team.
- Chr 17 has met the MP50 Challenge: the number of PE2,3,4 missing proteins coded on Chr 17 has been reduced from 148 to 87, meaning that 61 MPs have been detected and incorporated into neXtProt PE1.
- Chr X (Japan) also have enjoyed great success in identifying MPs, with 35 now PE1 proteins in neXt-Prot.
Nominations for Co-Chair of the HPP
A call for nominations for Co-Chair of the HPP (2021-01 – 2022-12) will be made soon. Please consider this position and do not be shy in nominations!
Please register and join us in HUPO Connect 2020 and donate to neXt-prot (https://www.hupo.org/Donate)
The C-HPP EC wish you and for all your family to stay safe and healthy and let’s go find proteomic evidence and clues for new cures!