1
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Browning TJ, Saito MA, Garaba SP, Wang X, Achterberg EP, Moore CM, Engel A, Mcllvin MR, Moran D, Voss D, Zielinski O, Tagliabue A. Persistent equatorial Pacific iron limitation under ENSO forcing. Nature 2023; 621:330-335. [PMID: 37587345 PMCID: PMC10499608 DOI: 10.1038/s41586-023-06439-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/14/2023] [Indexed: 08/18/2023]
Abstract
Projected responses of ocean net primary productivity to climate change are highly uncertain1. Models suggest that the climate sensitivity of phytoplankton nutrient limitation in the low-latitude Pacific Ocean plays a crucial role1-3, but this is poorly constrained by observations4. Here we show that changes in physical forcing drove coherent fluctuations in the strength of equatorial Pacific iron limitation through multiple El Niño/Southern Oscillation (ENSO) cycles, but that this was overestimated twofold by a state-of-the-art climate model. Our assessment was enabled by first using a combination of field nutrient-addition experiments, proteomics and above-water hyperspectral radiometry to show that phytoplankton physiological responses to iron limitation led to approximately threefold changes in chlorophyll-normalized phytoplankton fluorescence. We then exploited the >18-year satellite fluorescence record to quantify climate-induced nutrient limitation variability. Such synoptic constraints provide a powerful approach for benchmarking the realism of model projections of net primary productivity to climate changes.
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Affiliation(s)
- Thomas J Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
| | - Mak A Saito
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Shungudzemwoyo P Garaba
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Xuechao Wang
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Eric P Achterberg
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - C Mark Moore
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Anja Engel
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Dawn Moran
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Daniela Voss
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Oliver Zielinski
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- German Research Center for Artificial Intelligence (DFKI), Oldenburg, Germany
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Warnemünde, Germany
| | - Alessandro Tagliabue
- Department of Earth, Ocean, Ecological Sciences, University of Liverpool, Liverpool, UK
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2
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Paoletti MM, Fournier GP, Dolan EL, Saito MA. Metaproteogenomic Profile of a Mesopelagic Adenylylsulfate Reductase: Course-Based Discovery Using the Ocean Protein Portal. J Proteome Res 2023; 22:2871-2879. [PMID: 37607408 PMCID: PMC10476264 DOI: 10.1021/acs.jproteome.3c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Indexed: 08/24/2023]
Abstract
Adenylylsulfate reductase (Apr) is a flavoprotein with a dissimilatory sulfate reductase function. Its ability to catalyze the reverse reaction in sulfur oxidizers has propelled a complex phylogenetic history of transfers with sulfate reducers and made this enzyme an important protein in ocean sulfur cycling. As part of a graduate course, we analyzed metaproteomic data from the Ocean Protein Portal and observed evidence of Apr alpha (AprA) and beta (AprB) subunits in the Central Pacific Ocean. The protein was originally taxonomically attributed toChlorobium tepidum TLS, a green sulfur bacterium. However, our phylogenomic and oceanographic contextual analysis contradicted this label, instead showing that this protein is consistent with the genomic material from the newly discovered Candidatus Lambdaproteobacteriaclass, implying that the ecological role of this lineage in oxygen minimum twilight zones is underappreciated. This study illustrates how metaproteogenomic analysis can contribute to more accurate metagenomic/proteomic annotations and comprehensive ocean biogeochemical processes conducive to course-based research experiences.
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Affiliation(s)
- Madeline M. Paoletti
- Department
of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gregory P. Fournier
- Department
of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erin L. Dolan
- Department
of Biochemistry and Molecular Biology, University
of Georgia, B122 Life
Sciences Bldg, Athens, Georgia 30602, United States
| | - Mak A. Saito
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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3
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Webb EA, Held NA, Zhao Y, Graham ED, Conover AE, Semones J, Lee MD, Feng Y, Fu FX, Saito MA, Hutchins DA. Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades. ISME COMMUNICATIONS 2023; 3:15. [PMID: 36823453 PMCID: PMC9950141 DOI: 10.1038/s43705-023-00214-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/13/2022] [Accepted: 01/12/2023] [Indexed: 02/25/2023]
Abstract
The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.
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Affiliation(s)
- Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Noelle A Held
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Environmental Systems Science, ETH, Zurich, Switzerland
| | - Yiming Zhao
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Elaina D Graham
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Asa E Conover
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jake Semones
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael D Lee
- Blue Marble Space Institute of Science, NASA Ames Research Center, Mountain View, CA, 94035, USA
| | - Yuanyuan Feng
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Fei-Xue Fu
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mak A Saito
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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4
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Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proc Natl Acad Sci U S A 2022; 119:e2200014119. [PMID: 36067300 PMCID: PMC9477243 DOI: 10.1073/pnas.2200014119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
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5
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Simopoulos CMA, Figeys D, Lavallée-Adam M. Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies. Methods Mol Biol 2022; 2456:319-338. [PMID: 35612752 DOI: 10.1007/978-1-0716-2124-0_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Constant improvements in mass spectrometry technologies and laboratory workflows have enabled the proteomics investigation of biological samples of growing complexity. Microbiomes represent such complex samples for which metaproteomics analyses are becoming increasingly popular. Metaproteomics experimental procedures create large amounts of data from which biologically relevant signal must be efficiently extracted to draw meaningful conclusions. Such a data processing requires appropriate bioinformatics tools specifically developed for, or capable of handling metaproteomics data. In this chapter, we outline current and novel tools that can perform the most commonly used steps in the analysis of cutting-edge metaproteomics data, such as peptide and protein identification and quantification, as well as data normalization, imputation, mining, and visualization. We also provide details about the experimental setups in which these tools should be used.
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Affiliation(s)
- Caitlin M A Simopoulos
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
- School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.
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6
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Held NA, Sutherland KM, Webb EA, McIlvin MR, Cohen NR, Devaux AJ, Hutchins DA, Waterbury JB, Hansel CM, Saito MA. Mechanisms and heterogeneity of in situ mineral processing by the marine nitrogen fixer Trichodesmium revealed by single-colony metaproteomics. ISME COMMUNICATIONS 2021; 1:35. [PMID: 36739337 PMCID: PMC9723768 DOI: 10.1038/s43705-021-00034-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
The keystone marine nitrogen fixer Trichodesmium thrives in high-dust environments. While laboratory investigations have observed that Trichodesmium colonies can access the essential nutrient iron from dust particles, less clear are the biochemical strategies underlying particle-colony interactions in nature. Here we demonstrate that Trichodesmium colonies engage with mineral particles in the wild with distinct molecular responses. We encountered particle-laden Trichodesmium colonies at a sampling location in the Southern Caribbean Sea; microscopy and synchrotron-based imaging then demonstrated heterogeneous associations with iron oxide and iron-silicate minerals. Metaproteomic analysis of individual colonies by a new low-biomass approach revealed responses in biogeochemically relevant proteins including photosynthesis proteins and metalloproteins containing iron, nickel, copper, and zinc. The iron-storage protein ferritin was particularly enriched implying accumulation of mineral-derived iron, and multiple iron acquisition pathways including Fe(II), Fe(III), and Fe-siderophore transporters were engaged. While the particles provided key trace metals such as iron and nickel, there was also evidence that Trichodesmium was altering its strategy to confront increased superoxide production and metal exposure. Chemotaxis regulators also responded to mineral presence suggesting involvement in particle entrainment. These molecular responses are fundamental to Trichodesmium's ecological success and global biogeochemical impact, and may contribute to the leaching of particulate trace metals with implications for global iron and carbon cycling.
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Affiliation(s)
- Noelle A Held
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Kevin M Sutherland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Matthew R McIlvin
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Natalie R Cohen
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Alexander J Devaux
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - John B Waterbury
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Mak A Saito
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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7
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Rajczewski AT, Mehta S, Nguyen DDA, Grüning B, Johnson JE, McGowan T, Griffin TJ, Jagtap PD. A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). Clin Proteomics 2021; 18:15. [PMID: 33971807 PMCID: PMC8107781 DOI: 10.1186/s12014-021-09321-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. METHODS: In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). RESULTS Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639-peptide possibilities to 87 peptides that were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. CONCLUSION We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.
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Affiliation(s)
- Andrew T Rajczewski
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Dinh Duy An Nguyen
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Björn Grüning
- Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA.
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8
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Rajczewski AT, Mehta S, Nguyen DDA, Grüning BA, Johnson JE, McGowan T, Griffin TJ, Jagtap PD. A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.09.21251427. [PMID: 33688669 PMCID: PMC7941646 DOI: 10.1101/2021.02.09.21251427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.
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Affiliation(s)
- Andrew T. Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dinh Duy An Nguyen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Björn A. Grüning
- Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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9
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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] [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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10
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Affiliation(s)
- Suman S. Thakur
- Proteomics and Cell Signaling, Lab
W110, Centre for Cellular & Molecular
Biology, Habsiguda, Uppal
Road, Hyderabad 500 007, Telangana, India
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