gov.noaa.nmfs.inport:77622 eng UTF8 dataset Database National Centers for Coastal Ocean Science resourceProvider NCCOS Scientific Data Coordinator NCCOS.data@noaa.gov pointOfContact 2026-03-04T19:17:27 ISO 19115-2 Geographic Information - Metadata Part 2 Extensions for imagery and gridded data ISO 19115-2:2009(E) NCCOS Assessment: Dinoflagellate Proteomics on SCTLD Progression in Dry Tortugas across Multiple Species from September 2021-August 2022 SCTLD Dinoflagellate Proteomics in Dry Tortugas 2023 creation 2025 publication NOAA/NMFS/EDM 77622 https://www.fisheries.noaa.gov/inport/item/77622 WWW:LINK-1.0-http--link Full Metadata Record View the complete metadata record on InPort for more information about this dataset. information Woodley, Cheryl M 843-762-8862 843-762-8737 331 Fort Johnson Road Charleston SC 29412 USA cheryl.woodley@noaa.gov principalInvestigator Saunders, Janet janet.saunders@noaa.gov author https://www.ebi.ac.uk/pride WWW:LINK-1.0-http--link PRIDE database Log in to the PRIDE website using the following details: Project accession: PXD057860 Token: PeOqkrOZVgyl Alternatively, reviewer can access the dataset by logging in to the PRIDE website using the following account details: Username: reviewer_pxd057860@ebi.ac.uk Password: rqmJNj9OTQWY download tableDigital This dataset is compromised of proteomic results from dinoflagellates isolated from four species of stony coral (Orbicella faveolata, Orbicella franksi, Montastraea cavernosa, and Colpophyllia natans) collected in Dry Tortugas over the course of a year during the onset of stony coral tissue loss disease (SCTLD) (Sept 2021 - Aug 2022). This project was the proteomics portion of a larger project done with the goal of identifying predictive markers of stony coral tissue loss disease (SCTLD) using dinoflagellate samples collected in Dry Tortugas during the initial onset of disease. completed NCCOS Scientific Data Coordinator NCCOS.data@noaa.gov custodian notPlanned EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > CNIDARIANS > ANTHOZOANS/HEXACORALS > HARD OR STONY CORALS theme Global Change Master Directory (GCMD) Science Keywords 17.0 Water Oceans and Coasts Theme theme NGDA Portfolio Themes Colpophyllia natans Dinoflagellata Montastraea cavernosa Orbicella faveolata Orbicella franksi theme World Register of Marine Species (WoRMS) CONTINENT > NORTH AMERICA > UNITED STATES OF AMERICA > FLORIDA CONTINENT > NORTH AMERICA > UNITED STATES OF AMERICA > FLORIDA > FLORIDA KEYS place Global Change Master Directory (GCMD) Location Keywords 20.8 MASS SPECTROMETERS > MASS SPECTROMETERS instrument Global Change Master Directory (GCMD) Instrument Keywords 17.2 Analytical Lab platform Global Change Master Directory (GCMD) Platform Keywords 17.2 Genetic Data Sets > Proteomic Analysis theme CoRIS Discovery Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular and Genetic Analysis > Proteomic Analysis theme CoRIS Theme Thesaurus NCCOS Research Data Type > Derived Data Product NCCOS Research Data Type > Field Observation NCCOS Research Data Type > Long-term Monitoring NCCOS Research Location > Geographic Areas > Coral Reefs NCCOS Research Location > Marine Protected Areas > National Parks NCCOS Research Location > Region > Atlantic Ocean NCCOS Research Location > U.S. States and Territories > Florida NCCOS Research Priority > Coastal Change: Vulnerability, Mitigation, and Restoration NCCOS Research Topic > Coral Reefs theme NCCOS Discovery Keywords DOC/NOAA/NOS/NCCOS > National Centers for Coastal Ocean Science, National Ocean Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 2017-04-24 publication 8.5 Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA) https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords GCMD Keyword Forum Page Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords information custodian Coral Health and Disease Studies project InPort otherRestrictions Cite As: National Centers for Coastal Ocean Science, [Date of Access]: NCCOS Assessment: Dinoflagellate Proteomics on SCTLD Progression in Dry Tortugas across Multiple Species from September 2021-August 2022 [Data Date Range], https://www.fisheries.noaa.gov/inport/item/77622. NOAA provides no warranty, nor accepts any liability occurring from any incomplete, incorrect, or misleading data, or from any incorrect, incomplete, or misleading use of the data. It is the responsibility of the user to determine whether or not the data is suitable for the intended purpose. license These data were produced by NOAA and are not subject to copyright protection in the United States. NOAA waives any potential copyright and related rights in these data worldwide through the Creative Commons Zero 1.0 Universal Public Domain Dedication (CC0-1.0). SPDX License: Creative Commons Zero v1.0 Universal (CC0-1.0) otherRestrictions Access Constraints: Will become publicly available after publication of a peer-reviewed manuscript otherRestrictions Use Constraints: none unclassified none none NOAA Data Management Plan (DMP) NOAA/NMFS/EDM 77622 https://www.fisheries.noaa.gov/inportserve/waf/noaa/nos/nccos/dmp/pdf/77622.pdf WWW:LINK-1.0-http--link NOAA Data Management Plan (DMP) NOAA Data Management Plan for this record on InPort. information crossReference eng; US oceans Sampling Instrument: Orbitrap Fusion Lumos LC-MS/MS Software: MaxQuant -82.9283 -82.844802 24.613802 24.678371 Dry Tortugas 2021-09-01 2022-08-01 false eng false Project accession: PXD057860 XML (Structured Text) Zip National Institutes of Health, National Center for Biotechnology Information, Gene Expression Omnibus geo@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/geo/ WWW:LINK-1.0-http--link Website Home Page Homepage for the organization. information Proteome Xchange http://www.ebi.ac.uk/pride Email: pride-support@ebi.ac.uk distributor https://www.ebi.ac.uk/pride/archive/projects/PXD057860/private WWW:LINK-1.0-http--link Proteomic Raw Data Raw Proteomic Characterization Data from four species of coral collected over the course of a year, during which time, the onset of stony coral tissue loss disease was monitored. download dataset Representativeness Data represents dinoflagellates isolated from four species of stony coral from Dry Tortuga regions that were present during the onset of SCTLD. Samples were collected from the same colonies over a one year period to give a full representation across temporal changes. These data were generated after collecting samples from multiple Orbicella faveolata, Orbicella franksi, Montastraea cavernosa, Colpophyllia natans colonies in September 2021, February 2022, June 2022, and August 2022 Samples were collected in Dry Tortugas and frozen for molecular analysis Dinoflagellates were extracted from coral tissue using 10% SDS solution with centrifugation. Saunders, Janet janet.saunders@noaa.gov processor Dinoflagellate homogenates were crushed and placed in lysis buffer (5% SDS with protease inhibitors). The proteins were extracted by tip sonicating on ice and then centrifuged at 2,000 rcf for 5 minutes. The supernatant was transferred to a new tube and then centrifuged at 10,000 rcf for 10 minutes. The supernatant was transferred to a new tube and 50 ul was reserved for protein quantification. Protein was quantified using Pierce BCA Protein Assay Kit. Saunders, Janet janet.saunders@noaa.gov processor Based on quantification, a volume equivalent to 100 ug was diluted to a volume of 80 ul in 5% SDS. Samples were reduced with 10 ul DTT at 60*C for 10 minutes. After cooling to room temperature (10 minutes), samples were alkylated with calcium acetamide and incubating in dark for 30 minutes. Alkylation was quenched by adding 12% phosphoric acid. Protein samples were digested following Protofi's S-trap protocol, using a 1:20 trypsin:sample ratio and incubating for 2 hours at 47*C. The resulting peptides were evaporated until dry and resuspended in 100 ul 0.1% formic acid in water. Peptide concentration was quantified using Pierce Quantitative Fluorometric Peptide Assay kit. Saunders, Janet janet.saunders@noaa.gov processor Peptides in solution were sent to University of Arkansas and analyzed using LC-MS/MS analysis. Peptide and proteins were identified using Mascot running against a known Orbicella faveolata annotated metagenome. Resulting search data was imported to Scaffold and identifications were accepted at <1% local FDR for peptides and proteins. Normalized spectral abundance factor was derived from normalized spectral counts and intensity based on absolute quantification (iBAQ) intensity data. Saunders, Janet janet.saunders@noaa.gov processor Source Contribution: Individual coral colonies were sampled multiple times over the course of a year (September 2021 - August 2022) to collect samples prior to lesion formation due to disease, and then sampled at the onset of lesion formation. This work was completed by Dr. Grace Klinges (gklinges@asu.edu) Collection of Coral Samples in Dry Tortugas Grace Klinges originator 2021-09 2022-08 Source Contribution: Frozen coral tissue samples were shipped to Dr. Woodley's lab (NOAA) at Hollings Marine Lab (Charleston, SC). The coral tissue was digested to initially isolate dinoflagellates from coral tissue. Protein from dinoflagellates was isolated and these proteins were digested to obtain trypsinized peptides for proteomic characterization. Protein Extraction from Dinoflagellates Cheryl Woodley originator Source Contribution: Digested peptides were analyzed at University of Arkansas IDEA National Resource for Quantitative Proteomics to characterize the peptides in the coral tissue. The data was run against an Orbicella fasta file and sent back to Dr. Woodley's lab for further analysis Proteomic Characterization IDEA National Resource for Quantitative Proteomcis (UMAS) https://www.idearesourceproteomics.org WWW:LINK-1.0-http--link IDEA National Resource for Quantative Proteomics website for IDEA information originator otherRestrictions otherRestrictions Access Constraints: none | Use Constraints: none Orbitrap Fusion Lumos LC-MS/MS LC-MS/MS MaxQuant Software MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. Orbitrap Fusion Lumos LC-MS/MS LC-MS/MS