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METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses.
Saunders, Jaclyn K; Gaylord, David A; Held, Noelle A; Symmonds, Nicholas; Dupont, Christopher L; Shepherd, Adam; Kinkade, Danie B; Saito, Mak A.
  • Saunders JK; Woods Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States.
  • Gaylord DA; Woods Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States.
  • Held NA; Woods Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States.
  • Symmonds N; Woods Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States.
  • Dupont CL; J. Craig Venter Institute, San Diego, La Jolla, California 92037, United States.
  • Shepherd A; Woods Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States.
  • Kinkade DB; Woods Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States.
  • Saito MA; Woods Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States.
J Proteome Res ; 19(11): 4718-4729, 2020 11 06.
Article in English | MEDLINE | ID: covidwho-748160
ABSTRACT
We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the least common ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https//metatryp.whoi.edu). Major expansion of the marine METATRYP database with predicted proteomes from environmental sequencing confirms a low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed to facilitate ocean metaproteomics and has been integrated into the Ocean Protein Portal (https//oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https//metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa analyzed, sharing <1% peptides with taxa outside of the betacoronavirus group, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Coronavirus / Proteome / Metagenomics / Aquatic Organisms Type of study: Prognostic study Limits: Humans Language: English Journal: J Proteome Res Journal subject: Biochemistry Year: 2020 Document Type: Article Affiliation country: Acs.jproteome.0c00385

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Coronavirus / Proteome / Metagenomics / Aquatic Organisms Type of study: Prognostic study Limits: Humans Language: English Journal: J Proteome Res Journal subject: Biochemistry Year: 2020 Document Type: Article Affiliation country: Acs.jproteome.0c00385