Shotgun proteomics of thermally challenged Caribbean reef corals (NCEI Accession 0227133)
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title: Shotgun proteomics of thermally challenged Caribbean reef corals (NCEI Accession 0227133)
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date: 2021-07-30
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abstract: A proteome profiling approach was taken to characterize the cellular biology of massive corals of the Upper Florida Keys exposed to experimentally elevated temperatures. Specifically, Orbicella faveolata specimens from two inshore (Cheeca Rocks & The Rocks) and one offshore reef (Little Conch) were incubated at either 33°C for 5 days or 32°C days for 31 days (with controls maintained at 30°C), and proteins were extracted from a subset of 16 samples (representing multiple coral genotypes at each temperature x time), separated by liquid chromatography, and sequenced by mass spectrometry (MS). The associated, open-access manuscript (Mayfield et al. 2021) includes all methodological details needed to interpret the proteomic data. However, I have nevertheless reiterated the majority of these details in this document to aid those in navigating the NCEI data submission. Alongside this detailed methodological treatise, I have also uploaded 16 RAW files generated by the MS (Q Exactive™, Thermo-Fisher Scientific [TFS]), 16 MZML (open-access MS mass peaks) files, 16 MZID (open-access MS results) files, two sequence libraries needed to query the proteomic data (fasta files for the coral host & its dinoflagellate [family Symbiodiniaceae] endosymbionts), and a tab-delimited “online supplemental data file” (OSDF) that 1) describes which samples were analyzed; 2) defines MS jargon and explains how to interpret the MS output; and 3) presents all data in a distilled format that is more amenable to analysis by traditional statistical approaches. Please note that there are 32 MZID files, rather than 16, because each of the 16 MZML files was separately queried against each of the two aforementioned fasta sequence libraries.
purpose: These data were collected to better understand how reef-building corals respond to elevated temperatures at the cellular level.
credit: Related Funding Agency: National Oceanic and Atmospheric Administration
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title: Mayfield, A. B., Aguilar, C., Kolodziej, G., Enochs, I. C., & Manzello, D. P. (2021). Shotgun Proteomic Analysis of Thermally Challenged Reef Corals. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.660153
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function: (CI_OnLineFunctionCode) download
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dataQualityInfo: (DQ_DataQuality)
scope: (DQ_Scope)
level: (MD_ScopeCode) dataset
lineage: (LI_Lineage)
processStep: (LE_ProcessStep)
description: NCEI Accession 0227133 v1.1 was published.
dateTime:
DateTime: 2021-07-30T21:07:44Z
output: (LE_Source)
sourceCitation: (CI_Citation)
title: NCEI Accession 0227133 v1.1
date: (CI_Date)
date: (inapplicable)
dateType: (CI_DateTypeCode) publication
citedResponsibleParty: (CI_ResponsibleParty)
individualName: (inapplicable)
contactInfo: (CI_Contact)
onlineResource: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/0227133/1.1
protocol: HTTPS
name: NCEI Accession 0227133 v1.1
description: published 2021-07-30T21:07:44Z
function: (CI_OnLineFunctionCode) download
role: (inapplicable)
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dataQualityInfo: (DQ_DataQuality)
scope: (DQ_Scope)
level: (MD_ScopeCode) dataset
lineage: (LI_Lineage)
processStep: (LE_ProcessStep)
description: Parameter or Variable: protein concentrations (measured); Units: presence/absence (0/1); Observation Category: laboratory analysis; Sampling Instrument: SCUBA diver; Sampling and Analyzing Method: A "shotgun" proteomics approach was taken in which proteins were purified, digested, separated (by nano-liquid chromatography), and sequenced (by mass spectrometry). Proteins were scored as either being present (1) or absent (0) from a sample.; Data Quality Method: A detailed treatise on quality control has been provided in the document "Mayfield et al. supplemental material." Briefly and non-exhaustively, we filtered out proteins found only in 1-2 of all samples..
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metadataMaintenance: (MD_MaintenanceInformation)
maintenanceAndUpdateFrequency: (MD_MaintenanceFrequencyCode) asNeeded
maintenanceNote: Metadata are developed, maintained and distributed by NCEI. Updates are performed as needed to maintain currentness.
contact: (CI_ResponsibleParty)
organisationName: NOAA National Centers for Environmental Information
role: (CI_RoleCode) custodian
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acquisitionInformation: (MI_AcquisitionInformation)
instrument: (MI_Instrument)
identifier: (MD_Identifier)
code: chromatograph
type: chromatograph
description: Gas, ion, liquid or other chromatograph
instrument: (MI_Instrument)
identifier: (MD_Identifier)
code: mass spectrometer
type: mass spectrometer
description: Instrument that measure the massess and relative concentrations of atoms and molecules