Testing for the Corona-2 (COVID-19) virus has utilized RNA and antibody analytical methodologies to date. However, there has been recent interest in the potential application of mass spectrometry based proteomic methods as a complement to these methods, which could improve throughput and provide additional capacity for testing during the pandemic. This website has been generated to aid in assay design by utilizing the METATRYP software to determine uniqueness of peptides that can be targeted in diagnostic assays.
METATRYP allows users to investigate the occurrance of tryptic peptides within the protein coding sequences predicted from genomes. This web interface allows users to select their search against a custom database created from selected genomes, with an emphasis on Riboviruses (specifically, coronaviruses), model host systems, oral microbiome microbes and common contaminants. The current list of predicted proteomes can be found on the database contents page https://metatryp-coronavirus.whoi.edu/database. The entire database was last updated on Nov. 22nd, 2020 from NCBI and the Coronaviridae potion of the database was again updated on Feb. 23, 2021. All Identical Protein Groups from the Coronaviridae (NCBI taxid: 11118) have been included in this update. Inlfuenza C & D proteins were also added with this update.
Occurrence of shared peptides across all the proteomes has been pre-computed. An interactive visualization of the frequency of shared tryptic peptides across the proteomes in the database is available in a heatmap format found by clicking on the logo below:
An example search with the SARS-CoV-2 coronavirus surface glycoprotein can be found at https://metatryp-coronavirus.whoi.edu/examples.
METATRYP was designed to allow users to investigate the specificity of tryptic peptides being considering in the design of targeted biomarker assays in targeted metaproteomic research. The publication describing METATRYP v. 2.0 with applications to coronavirus can be found at https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00385. The original publication and description for METATRYP v. 1.0 can be found at http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400630/abstract, an example scientific application of METATRYP can be found at http://science.sciencemag.org/content/345/6201/1173. The software and documentation for METATRYP v. 2.0 is available here https://github.com/WHOIGit/metatryp-2.0.
Users developing diagnostic assays should take care to independently confirm their informatic analyses, as the METATRYP Coronavirus instance is intended as a software example and the current database may not be maintained as further sequence data emerges.
This site and the METATRYP software were developed for the Ocean Protein Portal project (https://www.oceanproteinportal.org) and funded by the EarthCube program of the US National Science Foundation and the Marine Microbial Initiative at Gordon and Betty Moore Foundation. Feedback and requests for additions to the web-based metatryp coronavirus database can be sent to metatryp@whoi.edu.Search for Peptide(s)
Seperate sequences by commas or carriage returns.