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Saito MA, Saunders JK, Chagnon M, Gaylord DA, Shepherd A, Held NA, Dupont C, Symmonds N, York A, Charron M, Kinkade DB. Development of an Ocean Protein Portal for Interactive Discovery and Education. J Proteome Res 2020; 20:326-336. [PMID: 32897077 DOI: 10.1021/acs.jproteome.0c00382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery of numerous aspects of microbial biogeochemical processes. However, these datasets present big data challenges as they often involve many samples collected across broad geospatial and temporal scales, resulting in thousands of protein identifications, abundances, and corresponding annotation information. The Ocean Protein Portal (OPP) was created to enable data sharing and discovery among multiple scientific domains and serve both research and education functions. The portal focuses on three use case questions: "Where is my protein of interest?", "Who makes it?", and "How much is there?" and provides profile and section visualizations, real-time taxonomic analysis, and links to metadata, sequence analysis, and other external resources to enable connections to be made between biogeochemical and proteomics datasets.
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Affiliation(s)
- Mak A Saito
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Jaclyn K Saunders
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Michael Chagnon
- RPS Group, South Kingston, Rhode Island 02879, United States.,Kaimika Technology, Cumberland, Rhode Island 02864, United States
| | - David A Gaylord
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Adam Shepherd
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Noelle A Held
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Christopher Dupont
- Woods Hole Oceanographic Institute, Falmouth, Massachusetts 02543, United States
| | - Nicholas Symmonds
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Amber York
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Matthew Charron
- Kaimika Technology, Cumberland, Rhode Island 02864, United States
| | - Danie B Kinkade
- Woods Hole Oceanographic Institute, Falmouth, Massachusetts 02543, United States
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Saunders JK, Gaylord DA, Held NA, Symmonds N, Dupont CL, Shepherd A, Kinkade DB, Saito MA. 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. J Proteome Res 2020; 19:4718-4729. [PMID: 32897080 PMCID: PMC7640959 DOI: 10.1021/acs.jproteome.0c00385] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Indexed: 12/30/2022]
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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Affiliation(s)
- Jaclyn K. Saunders
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States
| | - David A. Gaylord
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States
| | - Noelle A. Held
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States
| | - Nicholas Symmonds
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States
| | | | - Adam Shepherd
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States
| | - Danie B. Kinkade
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States
| | - Mak A. Saito
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road Mailstop #51, Woods Hole, Massachusetts 02543, United States
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Saito MA, Bertrand EM, Duffy ME, Gaylord DA, Held NA, Hervey WJ, Hettich RL, Jagtap PD, Janech MG, Kinkade DB, Leary DH, McIlvin MR, Moore EK, Morris RM, Neely BA, Nunn BL, Saunders JK, Shepherd AI, Symmonds NI, Walsh DA. Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. J Proteome Res 2019; 18:1461-1476. [PMID: 30702898 DOI: 10.1021/acs.jproteome.8b00761] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, colimitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Yet challenges remain for ocean metaproteomics due to the great biological diversity that produces highly complex mass spectra, as well as the difficulty in obtaining and working with environmental samples. This review summarizes the progress and challenges facing ocean metaproteomic scientists and proposes best practices for data sharing of ocean metaproteomic data sets, including the data types and metadata needed to enable intercomparisons of protein distributions and annotations that could foster global ocean metaproteomic capabilities.
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Affiliation(s)
- Mak A Saito
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Erin M Bertrand
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Megan E Duffy
- School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - David A Gaylord
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Noelle A Held
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | | | - Robert L Hettich
- Oak Ridge National Laboratory and Microbiology Department , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Saint Paul , Minnesota 55108 , United States
| | - Michael G Janech
- College of Charleston , Charleston , South Carolina 29424 , United States
| | - Danie B Kinkade
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Dagmar H Leary
- U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States
| | - Matthew R McIlvin
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Eli K Moore
- Department of Environmental Science , Rowan University , Glassboro , New Jersey 08028 , United States
| | - Robert M Morris
- School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - Benjamin A Neely
- National Institute of Standards and Technology , Charleston , South Carolina 29412 , United States
| | - Brook L Nunn
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Jaclyn K Saunders
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States.,School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - Adam I Shepherd
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Nicholas I Symmonds
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - David A Walsh
- Department of Biology , Concordia University , Montreal , Quebec H4B 1R6 , Canada
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