Summary of Study ST002460

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 PR001587. The data can be accessed directly via it's Project DOI: 10.21228/M8JX4P 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 IDST002460
Study TitlePaleamon metabolomics
Study Typemetabolomics
Study SummaryThe prawn Palaemon serratus exhibits a large distribution (occurring along the Northeastern Atlantic coast to the Mediterranean), and has thus been found suitable as model organism valuable for various ecotoxicological studies. However, little is still known about the potential input of its metabolome and particularly concerning a potential molecular sexual dimorphism observable in the different tissues of this organism. In an ecotoxicological point of view, inter-sex and inter-organ differences of the metabolomes may introduce analytical bias and impact the robustness of the analysis and its interpretation. To explore such possibilities, we obtained qualitative metabolomic data from the analysis of different organs of mature male and female Palaemon serratus. We used ultra-high-performance liquid chromatography-electrospray ionization-high resolution tandem mass spectrometry (UHPLC-ESI-HRMS on positive mode) to characterize the 75%-extracted metabolome of both gills, hepatopancreas, nervous gland, muscle and gonads.
Institute
National Museum of Natural History
DepartmentAviv
LaboratoryUMR 7245 MCAM
Last NameMarie
First NameBenjamin
Address12 rue Buffon 75005 Paris - France
Emailbmarie@mnhn.fr
Phone331 40 79 32 12
Submit Date2023-01-26
Num Groups10
Total Subjects100
Num Males50
Num Females50
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-02-15
Release Version1
Benjamin Marie Benjamin Marie
https://dx.doi.org/10.21228/M8JX4P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001587
Project DOI:doi: 10.21228/M8JX4P
Project Title:Palaemon metabolomics
Project Type:Metabolomics
Project Summary:The prawn Palaemon serratus exhibits a large distribution (occurring along the Northeastern Atlantic coast to the Mediterranean), and has thus been found suitable as model organism valuable for various ecotoxicological studies. However, little is still known about the potential input of its metabolome and particularly concerning a potential molecular sexual dimorphism observable in the different tissues of this organism. In an ecotoxicological point of view, inter-sex and inter-organ differences of the metabolomes may introduce analytical bias and impact the robustness of the analysis and its interpretation. To explore such possibilities, we obtained qualitative metabolomic data from the analysis of different organs of mature male and female Palaemon serratus. We used ultra-high-performance liquid chromatography-electrospray ionization-high resolution tandem mass spectrometry (UHPLC-ESI-HRMS on positive mode) to characterize the 75%-extracted metabolome of both gills, hepatopancreas, nervous gland, muscle and gonads.
Institute:National Museum of Natural History
Department:Aviv
Laboratory:UMR 7245 MCAM
Last Name:Marie
First Name:Benjamin
Address:12 rue Buffon 75005 Paris - France
Email:bmarie@mnhn.fr
Phone:331 40 79 32 12

Subject:

Subject ID:SU002550
Subject Type:Other organism
Subject Species:Palaemon serratus
Taxonomy ID:645159
Age Or Age Range:Adults
Weight Or Weight Range:10g
Height Or Height Range:5cm
Gender:Male and female

Factors:

Subject type: Other organism; Subject species: Palaemon serratus (Factor headings shown in green)

mb_sample_id local_sample_id Organ sex
SA24626720210712_Palaemon_Branchie_F9_69_01_10972Gills Female
SA24626820210712_Palaemon_Branchie_F10_70_01_10973Gills Female
SA24626920210712_Palaemon_Branchie_F1_61_01_10964Gills Female
SA24627020210712_Palaemon_Branchie_F7_67_01_10970Gills Female
SA24627120210712_Palaemon_Branchie_F8_68_01_10971Gills Female
SA24627220210712_Palaemon_Branchie_F6_66_01_10969Gills Female
SA24627320210712_Palaemon_Branchie_F2_62_01_10965Gills Female
SA24627420210712_Palaemon_Branchie_F4_64_01_10967Gills Female
SA24627520210712_Palaemon_Branchie_F3_63_01_10966Gills Female
SA24627620210712_Palaemon_Branchie_F5_65_01_10968Gills Female
SA24627720210712_Palaemon_Branchie_M7_77_01_10985Gills Male
SA24627820210712_Palaemon_Branchie_M8_78_01_10986Gills Male
SA24627920210712_Palaemon_Branchie_M9_79_01_10987Gills Male
SA24628020210712_Palaemon_Branchie_M6_76_01_10984Gills Male
SA24628120210712_Palaemon_Branchie_M10_80_01_10988Gills Male
SA24628220210712_Palaemon_Branchie_M5_75_01_10983Gills Male
SA24628320210712_Palaemon_Branchie_M1_71_01_10979Gills Male
SA24628420210712_Palaemon_Branchie_M2_72_01_10980Gills Male
SA24628520210712_Palaemon_Branchie_M4_74_01_10982Gills Male
SA24628620210712_Palaemon_Branchie_M3_73_01_10981Gills Male
SA24628720210712_Palaemon_Gonad_F7_47_01_10930Gonads Female
SA24628820210712_Palaemon_Gonad_F9_49_01_10932Gonads Female
SA24628920210712_Palaemon_Gonad_F6_46_01_10929Gonads Female
SA24629020210712_Palaemon_Gonad_F8_48_01_10931Gonads Female
SA24629120210712_Palaemon_Gonad_F4_44_01_10927Gonads Female
SA24629220210712_Palaemon_Gonad_F1_41_01_10924Gonads Female
SA24629320210712_Palaemon_Gonad_F2_42_01_10925Gonads Female
SA24629420210712_Palaemon_Gonad_F3_43_01_10926Gonads Female
SA24629520210712_Palaemon_Gonad_F10_50_01_10933Gonads Female
SA24629620210712_Palaemon_Gonad_F5_45_01_10928Gonads Female
SA24629720210712_Palaemon_Gonad_M4_54_01_10947Gonads Male
SA24629820210712_Palaemon_Gonad_M8_58_01_10951Gonads Male
SA24629920210712_Palaemon_Gonad_M9_59_01_10952Gonads Male
SA24630020210712_Palaemon_Gonad_M10_60_01_10953Gonads Male
SA24630120210712_Palaemon_Gonad_M7_57_01_10950Gonads Male
SA24630220210712_Palaemon_Gonad_M6_56_01_10949Gonads Male
SA24630320210712_Palaemon_Gonad_M3_53_01_10946Gonads Male
SA24630420210712_Palaemon_Gonad_M5_55_01_10948Gonads Male
SA24630520210712_Palaemon_Gonad_M2_52_01_10945Gonads Male
SA24630620210712_Palaemon_Gonad_M1_51_01_10944Gonads Male
SA24630720210712_Palaemon_HP_F7_7_01_11085Hepatopancreas Female
SA24630820210712_Palaemon_HP_F8_8_01_11086Hepatopancreas Female
SA24630920210712_Palaemon_HP_F9_9_01_11087Hepatopancreas Female
SA24631020210712_Palaemon_HP_F1_1_01_11079Hepatopancreas Female
SA24631120210712_Palaemon_HP_F6_6_01_11084Hepatopancreas Female
SA24631220210712_Palaemon_HP_F5_5_01_11083Hepatopancreas Female
SA24631320210712_Palaemon_HP_F2_2_01_11080Hepatopancreas Female
SA24631420210712_Palaemon_HP_F3_3_01_11081Hepatopancreas Female
SA24631520210712_Palaemon_HP_F4_4_01_11082Hepatopancreas Female
SA24631620210712_Palaemon_HP_F10_10_01_11088Hepatopancreas Female
SA24631720210712_Palaemon_HP_M2_12_01_11097Hepatopancreas Male
SA24631820210712_Palaemon_HP_M8_18_01_11103Hepatopancreas Male
SA24631920210712_Palaemon_HP_M9_19_01_11104Hepatopancreas Male
SA24632020210712_Palaemon_HP_M10_20_01_11105Hepatopancreas Male
SA24632120210712_Palaemon_HP_M7_17_01_11102Hepatopancreas Male
SA24632220210712_Palaemon_HP_M6_16_01_11101Hepatopancreas Male
SA24632320210712_Palaemon_HP_M4_14_01_11099Hepatopancreas Male
SA24632420210712_Palaemon_HP_M5_15_01_11100Hepatopancreas Male
SA24632520210712_Palaemon_HP_M3_13_01_11098Hepatopancreas Male
SA24632620210712_Palaemon_HP_M1_11_01_11096Hepatopancreas Male
SA24632720210712_Palaemon_muscle_F5_85_01_11003Muscle Female
SA24632820210712_Palaemon_muscle_F4_84_01_11002Muscle Female
SA24632920210712_Palaemon_muscle_F3_83_01_11001Muscle Female
SA24633020210712_Palaemon_muscle_F6_86_01_11004Muscle Female
SA24633120210712_Palaemon_muscle_F7_87_01_11005Muscle Female
SA24633220210712_Palaemon_muscle_F10_90_01_11008Muscle Female
SA24633320210712_Palaemon_muscle_F9_89_01_11007Muscle Female
SA24633420210712_Palaemon_muscle_F8_88_01_11006Muscle Female
SA24633520210712_Palaemon_muscle_F2_82_01_11000Muscle Female
SA24633620210712_Palaemon_muscle_F1_81_01_10999Muscle Female
SA24633720210712_Palaemon_muscle_M4_94_01_11022Muscle Male
SA24633820210712_Palaemon_muscle_M3_93_01_11021Muscle Male
SA24633920210712_Palaemon_muscle_M2_92_01_11020Muscle Male
SA24634020210712_Palaemon_muscle_M1_91_01_11019Muscle Male
SA24634120210712_Palaemon_muscle_M6_96_01_11024Muscle Male
SA24634220210712_Palaemon_muscle_M5_95_01_11023Muscle Male
SA24634320210712_Palaemon_muscle_M7_97_01_11025Muscle Male
SA24634420210712_Palaemon_muscle_M9_99_01_11027Muscle Male
SA24634520210712_Palaemon_muscle_M10_100_01_11028Muscle Male
SA24634620210712_Palaemon_muscle_M8_98_01_11026Muscle Male
SA24634720210712_Palaemon_GlandeNerveuse_F5_25_01_11043Nervous gland Female
SA24634820210712_Palaemon_GlandeNerveuse_F4_24_01_11042Nervous gland Female
SA24634920210712_Palaemon_GlandeNerveuse_F1_21_01_11039Nervous gland Female
SA24635020210712_Palaemon_GlandeNerveuse_F6_26_01_11044Nervous gland Female
SA24635120210712_Palaemon_GlandeNerveuse_F3_23_01_11041Nervous gland Female
SA24635220210712_Palaemon_GlandeNerveuse_F7_27_01_11045Nervous gland Female
SA24635320210712_Palaemon_GlandeNerveuse_F2_22_01_11040Nervous gland Female
SA24635420210712_Palaemon_GlandeNerveuse_F10_30_01_11048Nervous gland Female
SA24635520210712_Palaemon_GlandeNerveuse_F9_29_01_11047Nervous gland Female
SA24635620210712_Palaemon_GlandeNerveuse_F8_28_01_11046Nervous gland Female
SA24635720210712_Palaemon_GlandeNerveuse_M5_35_01_11063Nervous gland Male
SA24635820210712_Palaemon_GlandeNerveuse_M4_34_01_11062Nervous gland Male
SA24635920210712_Palaemon_GlandeNerveuse_M2_32_01_11060Nervous gland Male
SA24636020210712_Palaemon_GlandeNerveuse_M6_36_01_11064Nervous gland Male
SA24636120210712_Palaemon_GlandeNerveuse_M3_33_01_11061Nervous gland Male
SA24636220210712_Palaemon_GlandeNerveuse_M9_39_01_11067Nervous gland Male
SA24636320210712_Palaemon_GlandeNerveuse_M10_40_01_11068Nervous gland Male
SA24636420210712_Palaemon_GlandeNerveuse_M1_31_01_11059Nervous gland Male
SA24636520210712_Palaemon_GlandeNerveuse_M8_38_01_11066Nervous gland Male
SA24636620210712_Palaemon_GlandeNerveuse_M7_37_01_11065Nervous gland Male
Showing results 1 to 100 of 100

Collection:

Collection ID:CO002543
Collection Summary:Specimens of Palaemon serratus were collected by a professional fisherman (DYFLO) in February 2021, using special traps in the 2-nautical mile zone of the Cap of La Hève (Le Havre, Normandy, France). The collected prawns were returned to the laboratory within a maximum of 1 h, using 30 L-polypropylene tanks filled with artificial sea water (ASW; salinity of 33‰ from dissolution of TETRA SEA® salt, which is commonly used in maintenance of marine aquarium), in oxygenated conditions (Rollin et al., 2021). The prawns were transferred and kept into 80 L-aquariums that were connected to an ASW supply, and under constant aeration and filtration. Then, 10 mature males and gravid females (i.e. ovarian stage 4) of homogenous size (i.e. 8.5 ± 0.9 cm total length) and homogenous moult stage (i.e. D1’-D1’’) were anesthetized on ice and dissected. The gills, the nervous gland (i.e. eyestalks medulla and supra oesophageal ganglia), the muscle, the hepatopancreas and the gonads were weighted, individually frozen in liquid nitrogen and stored at -20°C.
Sample Type:Shrimp organs
Collection Method:Fishing net
Collection Location:Le Havre, France
Storage Conditions:-20℃
Storage Vials:eppendorfs

Treatment:

Treatment ID:TR002562
Treatment Summary:no treatment was applied. Individuals were anaesthetized and organs were collected, frozen and kept at -20°C prior to metabolite extraction.

Sample Preparation:

Sampleprep ID:SP002556
Sampleprep Summary:Metabolites were extracted from wet tissues with 75%-25% UHPLC methanol-water (with a ratio of 1 ml for 100 mg of fresh tissues), grinded mechanically (GLH850 OMNI) and sonicated with an ultrasonic probe (SONICS VibraCell, 130 Watt, 20 Khz, 60% amplitude) for 30 sec, twice. Samples were then centrifuged at 15,000 g for 10 min at 4°C and the supernatant collected and store at -20°C until mass spectrometry analysis.
Processing Storage Conditions:-20℃
Extract Storage:-20℃

Combined analysis:

Analysis ID AN004014
Analysis type MS
Chromatography type Reversed phase
Chromatography system Bruker ELUTE UHPLC
Column Thermo Acclaim Polar Advantage II (150 x 3mm,3um)
MS Type ESI
MS instrument type QTOF
MS instrument name Bruker Compact
Ion Mode POSITIVE
Units counts

Chromatography:

Chromatography ID:CH002965
Chromatography Summary:The metabolites were analysed by injection of 2 µL of the supernatants on an UHPLC (ELUTE, Bruker) using a Polar Advances II 2.5 pore C18 column (Thermo, Waltham, MA, USA) at a 300 µL·min−1 flow rate with a linear gradient of acetonitrile in 0.1% formic acid (5%–90% in 16 min).
Instrument Name:Bruker ELUTE UHPLC
Column Name:Thermo Acclaim Polar Advantage II (150 x 3mm,3um)
Column Temperature:40
Flow Gradient:5-90%
Flow Rate:0.3 mL/min
Solvent A:100% water
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS003761
Analysis ID:AN004014
Instrument Name:Bruker Compact
Instrument Type:QTOF
MS Type:ESI
MS Comments:Metabolites were subsequently ionised and analysed using an electrospray ionization hybrid quadrupole time-of-flight high-resolution mass spectrometer (ESI-Qq-TOF Compact, Bruker) at 2 Hz speed on the 50–1500 m/z range on positive autoMS/MS mode between 2 and 8 Hz speed on the 50–1500 m/z range with information-dependent acquisition (IDA).
Ion Mode:POSITIVE
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