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Highlight from HPP special issue in Journal of Proteome Research

26 Nov 2020 6:11 PM | Anonymous member (Administrator)

The Human Proteome Project (HPP) Special Issue in Journal of Proteome Research will be published on December 4, 2020, with more 15 articles and one editorial addressing different issues related to the human proteome. The Guest Editorial team comprising Drs. Young-Ki Paik, Gil Omenn, Lydie Lane, Eric Deutsch, Fernando Corrales, and Chris Overall (Associate Editor) were responsible for this 8th Special Issue.

- The Special Issue commences with the Annual HPP Metrics paper by Omenn et al 2020 (https://doi.org/10.1021/acs.jproteome.0c00485). The HPP metrics paper provides fine grain detail of progress and challenges in credibly identifying the human proteome over the past year.

- Two papers addressing the use of pluripotent stem cells (PSCs) to study function of uPE1 proteins, which proteins are well detected, but they have no single known molecular function by Frederik Edfors and Ghasem Salekdeh and colleagues (https://dx.doi.org/10.1021/acs.jproteome.0c00689).

- Kotol et al (https://dx.doi.org/10.1021/acs.jproteome.0c00194) used information derived from the Human Protein Atlas to devise a series of isotopically labelled peptides with corresponding PRM assays for the detection of 21 drug targets and biomarkers in human plasma.

- Insight into the First Phosphoproteomics challenge of the MS Resource Pillar by Rob Moritz and Sue Weintraub in Hoopmann et al (https://dx.doi.org/10.1021/acs.jproteome.0c00648). Standardised sets of 94 phosphopeptides were analysed by 22 laboratories using different approaches, MS instrumentation and bioinformatics. The data were reanalysed in a consistent manner that pointed out the challenges of correct phosphopeptide site identification.

- Bioinformatics approaches were developed as described in this special issue to tackle the uPE1 challenge include a guilt-by-association bioinformatics approach from the Spanish team in Gonzalez-Gomariz et al 2020 (https://dx.doi.org/10.1021/acs.jproteome.0c00364). In an innovative approach, the authors employed web search tools, such as the Google page rank algorithm, to develop UPEFinder. The Korean Chromosome 11 team used the successful I-TASSER/COFACTOR approach to predict 2,413 GO terms for 22 uPE1 chromosome 11 proteins (https://dx.doi.org/10.1021/acs.jproteome.0c00482).

- Ping Xu team used Open-pFind tool, which is an open modification search tool, which improves identification of peptide and proteins, and with this tool the authors identified peptides candidates for 103 missing proteins, from which 4 were validated in the study (https://doi.org/10.1021/acs.jproteome.0c00370) (China).

- From the Human Protein Atlas and the Antibody Resource Pillar comes the achievement of “enhanced validation” of nearly 6,000 antibodies directed towards 3,775 proteins in many tissues detailed by Sivertsson et al (https://dx.doi.org/10.1021/acs.jproteome.0c00486) (Sweden). This led to the localization of 56 candidate MPs and 171 uncharacterised PE1 proteins (uPE1) lacking any known function.

- Vandenbrouck et al 2020 (https://dx.doi.org/10.1021/acs.jproteome.0c00516) tackled the uPE1 neXt-CP50 Challenge in a cohort of 421 uPE1 proteins found in higher abundance in the male reproductive tract by compilation of diverse evidence. To functionally annotate such proteins, contextual information from the literature, protein-protein interactions, expression levels and cellular localization were employed in a knowledge-driven approach to suggest rational, knowledge-founded hypotheses that can be experimentally tested in a targeted manner with higher probability of incise results and less false starts.

- The Journal welcomes the new Chair of the HPP, Dr. Rob Moritz, Institute for Systems Biology, Seattle as a new Guest Editor for the 9th Annual Special Issue of the Journal of Proteome Research on the HPP in 2021.

Join us! Research teams for Chromosome 21 and 22!

C-HPP Consortium leadership is looking for partners, which can join C-HPP initiative to advance MP50 and CP50 projects by identifying missing proteins and identify function(s) to uPE1 proteins for chromosomes 21 and 22. Motivated PIs are encouraged to contact Chris Overall (Chair of C-HPP, email chris.overall@ubc.ca) or other members of the C-HPP leadership.

23rd C-HPP Workshop in Busan (South-Korea), June 28-30, 2021

Due to COVID-19 pandemic and related health risk and world-wide travel restrictions we had many meetings and workshops cancelled, amongst others the 23rd C-HPP Workshop originally planned in May 15-18, 2020 in Saint Petersburg, Russia. We hope that vaccine against SARS-CoV-2 viral infection will be available in early next year and our onsite meeting will be held in Summer 2021 as planned. Therefore, we would like to encourage you to plan on joining the 23rd C-HPP Workshop on June 28-30, 2021, in Busan, South Korea. This meeting is being organized in conjunction with Commemoration of the 20th Anniversary of AOHUPO (www.aohupo.org). The C-HPP EC will make you update on the preparation of this meeting with scientific programs through the websites of HUPO, C-HPP and C-HPP Wiki in addition to our routine email communications.

We wish you and your family to stay safe and healthy.

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