Ocean Protein Portal Updates METATRYP to Encompass COVID-19 Peptides Data
Shared peptides of SARS-CoV-2 with other key taxa are illustrated in this image. Credit: Jaclyn Saunders, Woods Hole Oceanographic Institution.
EarthCube is a community-driven activity sponsored by the National Science Foundation to transform research in the academic geosciences community. EarthCube aims to create a well-connected environment to share data and knowledge in an open, transparent, and inclusive manner, thus accelerating our ability to better understand and predict the Earth’s systems. EarthCube membership is free and open to anyone in the Geosciences, as well as those building platforms to serve the Earth Sciences. The EarthCube Office is led by the San Diego Supercomputer Center (SDSC) on the UC San Diego campus.
Kimberly Mann Bruch, San Diego Supercomputer Center Communications, firstname.lastname@example.org
Lynne Schreiber, San Diego Supercomputer Center EarthCube Office, email@example.com
Ocean Protein Portal: https://proteinportal.whoi.edu/
San Diego Supercomputer Center: https://www.sdsc.edu/
UC San Diego: https://ucsd.edu/
National Science Foundation: https://www.nsf.gov/
January 15, 2021
By: Kimberly Mann Bruch
EarthCube project researchers from Woods Hole Oceanographic Institution recently published their study findings related to SARS-CoV-2 coronavirus peptides in the Journal of Proteome Research. Specifically, the scientists discussed how SARS-CoV-2 has the most shared tryptic peptides with its closest bat precursor virus and while the COVID-19 strain has some shared peptides with SARS-CoV-1, it is very different from the “common influenza”.
The discovery was made possible by the Ocean Protein Portal’s METATRYP software, which allows users to query the occurrence of shared peptides encoded by various coronavirus genomes and other relevant taxa. "The METATRYP software focuses on short peptides which make up proteins, instead of full-length protein sequences, as peptides are the biological units directly measured with proteomics mass spectrometry methods,” said Jaclyn Saunders, postdoctoral investigator at Woods Hole Oceanographic Institution and lead author on the paper.
“METATRYP is a flexible software package to assess taxonomic occurrence of shared peptides applicable to proteomics studies of complex systems valuable for the identification of biomarkers and phyloproteomic analysis of complex communities,” further explained Mak Saito, co-principal investigator for the Ocean Protein Portal and senior scientist at Woods Hole Oceanographic Institution. “We created web portals for METATRYP that use specialized databases for the marine microbial research communities as well as the coronavirus research community.”
One of these databases focused on coronavirus strains and included a total of 94 coronavirus taxa along with other relevant taxa like the human proteome and common human pathogens and oral microbiome bacterial strains. Within this database, the researchers showed that the SARS-CoV-2 responsible for the ongoing COVID-19 pandemic is found in a separate cluster among these taxa, clustering most closely with bat-hosted coronaviruses. Additionally, the strain RaTG13 isolated from a bat is the most closely related strain and shares 84 percent of its peptides with SARS-CoV-2.
The Ocean Protein Portal is an EarthCube Data Capabilities program that is funded by the National Science Foundation under Award Number 2026933.