Summary of Study ST002385

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001535. The data can be accessed directly via it's Project DOI: 10.21228/M88T5J This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002385
Study TitleMetabolomics in small-spotted catshark reproduction- Seminal plasma Semi-polar
Study Summarythis study aimed to elucidate the influence of the environment (wild vs. aquarium) on the metabolic signatures in the seminal plasma (wild-captured vs. aquarium-housed).
Institute
Universidad CEU San Pablo
Last NameLorenzo Rebenaque
First NameLaura
AddressEd. Seminario. S/n, Moncada, Valencia, 46113, Spain
Emaillaura.lorenzorebenaque@uchceu.es
Phone615056012
Submit Date2022-11-27
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-12-30
Release Version1
Laura Lorenzo Rebenaque Laura Lorenzo Rebenaque
https://dx.doi.org/10.21228/M88T5J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001535
Project DOI:doi: 10.21228/M88T5J
Project Title:Metabolomics in Small-spotted catshark reproduction
Project Summary:This study aimed to elucidate the influence of the environment (wild vs. aquarium) on the metabolic signatures in the seminal plasma and peripheral blood plasma in small-spotted catshark (wild-captured vs. aquarium-housed).
Institute:Universidad CEU San Pablo
Last Name:Lorenzo Rebenaque
First Name:Laura
Address:Ed. Seminario. S/n, Moncada, Valencia, 46113, Spain
Email:laura.lorenzorebenaque@uchceu.es
Phone:615056012

Subject:

Subject ID:SU002474
Subject Type:Fish
Subject Species:Scyliorhinus canicula

Factors:

Subject type: Fish; Subject species: Scyliorhinus canicula (Factor headings shown in green)

mb_sample_id local_sample_id Group Sample
SA237994PO6aquarium-housed seminal plasma
SA237995PO1aquarium-housed seminal plasma
SA237996PO5aquarium-housed seminal plasma
SA237997PO7aquarium-housed seminal plasma
SA237998PO2aquarium-housed seminal plasma
SA237999PO4aquarium-housed seminal plasma
SA238000PO3aquarium-housed seminal plasma
SA238001PS9wild-captured seminal plasma
SA238002PS10wild-captured seminal plasma
SA238003PS12wild-captured seminal plasma
SA238004PS8wild-captured seminal plasma
SA238005PS11wild-captured seminal plasma
SA238006PS3wild-captured seminal plasma
SA238007PS2wild-captured seminal plasma
SA238008PS1wild-captured seminal plasma
SA238009PS4wild-captured seminal plasma
SA238010PS5wild-captured seminal plasma
SA238011PS6wild-captured seminal plasma
SA238012PS7wild-captured seminal plasma
Showing results 1 to 19 of 19

Collection:

Collection ID:CO002467
Collection Summary:Seminal plasma samples were collected and immediately snap frozen for metabolomics analysis at the end of experiment
Sample Type:Seminal plasma

Treatment:

Treatment ID:TR002486
Treatment Summary:Samples were collected from a total of 12 wild small-spotted catsharks from the Mediterranean Sea and 7 aquarium-housed small-spotted catsharks in collaboration with Oceanogràfic of Valencia. Location (wild vs. aquarium). Wild individuals were donated from local fisheries at the Valencian Community and were part of accidental captures intended to commercial fisheries ports at Valencia (39°26′45″N 0°19′12″O), Jávea (38°47′21″N 0°09′47″E) and Cullera port (39°09′58″N 0°15′10″O). Mediterranean Sea water parameters, measured by Valencia buoy (39º52′N0º20′E) were 14.6-19 °C temperature and 34-37 g/l salinity (http://www.puertos.es/es-es/oceanografia/Paginas/portus.aspx). Small-spotted catsharks under managed care were housed at Oceanogràfic of Valencia, Spain, in closed and recirculation system under controlled conditions, monitored water quality (17–21°C, 5.1 mg/l oxygen, 36 g/l salinity and 7.6–8.2 pH), fixed photoperiod (12:12 h) and disinfection using UV light and ozone.

Sample Preparation:

Sampleprep ID:SP002480
Sampleprep Summary:Seminal plasma were subjected to a comparative metabolomics analysis. For aquarium-housed individuals’ 7 samples of both types (Seminal plasma and peripheral blood plasma), were analysed to study the semi-polar and non-polar fractions. For wild-captured individuals’ 12 samples of both types (Seminal plasma and peripheral blood plasma), were analysed to study the semi-polar and non-polar fractions. For semi-polar analysis, metabolites were extracted from 100 μL of each Seminal plasma or peripheral blood plasma samples following a published method with a little modification (Y. Yu et al., 2021). Briefly, samples were dissolved in 200 μL of cold aqueous methanol (75 %), and 200 μL of acetronitrile (75 %), spiked with 10 μg/ml formononetin as internal standard. Then, the mixture was centrifugated at 20,000 xg for 15 min at 4 °C. The supernate (200 μL) was gained, and dried under low-temperature vacuum (Thermo Scientific, USA). The samples were redissolved resuspended with 100 μL of methanol (10 %) and transferred to HPLC tubes and an aliquot of 3 μL was injected for the analysis. For no-polar analysis, metabolites were extracted from 50 μL of each Seminal plasma or peripheral blood plasma samples following a published method with a little modification (Y. Yu et al., 2021). Briefly, samples were dissolved in 300 μL of cold aqueous methanol (100 %), spiked with 50 μg/ml alpha-tocopherol acetate as internal standard. Then, the mixture was swirled for 120 seconds, and 900 μL MTBE and 250 μL ultrapure water were added. After vortexed for 15 mins, the mixture was placed 30 min at 4 ℃. Then, the supernatants (900 μL) were gained, and dried under low-temperature vacuum (Thermo Scientific, USA). The samples were redissolved resuspended with 600 μL of acetonitrile–isopropanol mixture and transferred to HPLC tubes and an aliquot of 3 μL was injected for the analysis.

Combined analysis:

Analysis ID AN003885 AN003886
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Phenomenex Luna (100 x 2.1mm,2.5um) Phenomenex Luna (100 x 2.1mm,2.5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units m/z ratio m/z ratio

Chromatography:

Chromatography ID:CH002879
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Luna (100 x 2.1mm,2.5um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003625
Analysis ID:AN003885
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For the untargeted metabolomic analysis, Compound Discoverer software (Thermofisher Scientific) was used to identify the peaks, peak filtration, and peak alignment, and performed chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses (m/z).
Ion Mode:POSITIVE
  
MS ID:MS003626
Analysis ID:AN003886
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For the untargeted metabolomic analysis, Compound Discoverer software (Thermofisher Scientific) was used to identify the peaks, peak filtration, and peak alignment, and performed chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses (m/z).
Ion Mode:NEGATIVE
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