Summary of Study ST001165

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000727. The data can be accessed directly via it's Project DOI: 10.21228/M8Q38G This work is supported by NIH grant, U2C- DK119886.


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Study IDST001165
Study TitlePhysiological and metabolic response of crab megalopae and juveniles to ocean acidification (part-III)
Study SummaryYoung crab samples were placed into 1 of 4 treatment groups to understand their metabolic response to ocean acidification and dissolved oxygen content.
DepartmentCB Division
Last NameNichols
First NameKrista
Submit Date2019-04-05
Analysis Type DetailLC-MS
Release Date2019-05-15
Release Version1
Krista Nichols Krista Nichols application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR000727
Project DOI:doi: 10.21228/M8Q38G
Project Title:GC analysis of crab megalopae and juveniles in response to ocean acidification
Project Summary:The objective of the study was to examine the physiological and metabolic response of crab megalopae and juveniles to ocean acidification treatment.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Phone:(530) 754-8258


Subject ID:SU001230
Subject Type:Invertebrate
Subject Species:Metacarcinus magister
Taxonomy ID:29965


Subject type: Invertebrate; Subject species: Metacarcinus magister (Factor headings shown in green)

mb_sample_id local_sample_id ph treatment DO treatment
SA080568M3A4High High
SA080569M3A5High High
SA080570M13B2High High
SA080571M13C7High High
SA080572M13B7High High
SA080573M3C4High High
SA080574M13D5High High
SA080575M3C5High High
SA080576M7D7High High
SA080577M7D1High High
SA080578M7C6High High
SA080579M7B5High High
SA080580M7A1High High
SA080581M13A6High High
SA080582M3B5High High
SA080583M6B4High Low
SA080584M12B5High Low
SA080585M6C3High Low
SA080586M6D5High Low
SA080587M6B2High Low
SA080588M6A6High Low
SA080589M6A3High Low
SA080590M12A3High Low
SA080591M12D6High Low
SA080592M12D1High Low
SA080593M12C7High Low
SA080594M12D2High Low
SA080595M12D3High Low
SA080596M6C4High Low
SA080597M12D7High Low
SA080598M5D4Low High
SA080599M8A6Low High
SA080600M8C6Low High
SA080601M8B2Low High
SA080602M8D7Low High
SA080603M8B3Low High
SA080604M5A7Low High
SA080605M10B3Low High
SA080606M10A5Low High
SA080607M10C2Low High
SA080608M5A4Low High
SA080609M5D7Low High
SA080610M10D5Low High
SA080611M5C5Low High
SA080612M10A1Low High
SA080613M11B3Low Low
SA080614M11B5Low Low
SA080615M11D5Low Low
SA080616M1B4Low Low
SA080617M11B1Low Low
SA080618M11A3Low Low
SA080619M1C1Low Low
SA080620M1A5Low Low
SA080621M4C5Low Low
SA080622M4D6Low Low
SA080623M4C2Low Low
SA080624M4B5Low Low
SA080625M11A6Low Low
SA080626M4A5Low Low
SA080627M1D1Low Low
Showing results 1 to 60 of 60


Collection ID:CO001224
Collection Summary:After each crab completed the treatment for the predetermined length of time, crabs were frozen whole specimen at -80°C and shipped to the West Coast Metabolomics Center.
Sample Type:Whole Animal


Treatment ID:TR001245
Treatment Summary:15 crabs were placed into 1 of 4 treatment groups: High pH:High Dissolved Oxygen, High pH:Low Dissolved Oxygen, Low pH:Low Dissolved Oxygen, Low pH: High Dissolved Oxygen. Crabs were subjected to their treatment group for 30-33 days.

Sample Preparation:

Sampleprep ID:SP001238
Sampleprep Summary:15mg of whole crab was placed into a 1.5mL ependorph tube. 2 x 3mm grinding beads were added to each sample. 225 µL of cold MeOH with quality controls was added to each samples. Batches of samples were ground with GenoGrinder for 30 seconds at 1500 rpm. 750µL of methyl tert-butyl Ether (MTBE) was added to each sample. Samples were vortexed for 10 seconds and then shaken at 4°C for 5 minutes using an Orbital Mixer. 188 uL of LC-MS grade water was added to each sample. Vortex for 10 seconds and then centrifuged for 2 minutes at 14,000 rcf. 2 x 350µL aliquots were removed from the top, organic layer, one submitted for analysis and the other stored as backup in -20°C. 2 x 125µL aliquots were removed from the bottom, polar layer, one submitted for analysis, the other stored at -20°C for backup.
Sample Resuspension:After drying, samples were resuspended in 110 µL of 9:1 methanol:toulene with 50 nM CUDA as an internal standard. Samples were vortexed for 10 seconds, then sonicated in room temperature water for 5 minutes, then centrifuged at 16,100 rcf for 2 minutes. 50 µL of the supernatant was removed and placed in an amber vial for lipidomics analysis.

Combined analysis:

Analysis ID AN001926 AN001927
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 UPLC Agilent 1290 UPLC
Column Waters Acquity CSH C18 2.1x10 0mm 1.7m Waters Acquity CSH C18 2.1x10 0mm 1.7m
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF
Units Peak Height Peak Height


Chromatography ID:CH001398
Instrument Name:Agilent 1290 UPLC
Column Name:Waters Acquity CSH C18 2.1x10 0mm 1.7m
Column Pressure:500-1000bar
Column Temperature:65°C
Flow Rate:600µL/min
Sample Injection:1.67µL
Chromatography Type:Reversed phase


MS ID:MS001782
Analysis ID:AN001926
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Comments:N/A
MS ID:MS001783
Analysis ID:AN001927
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Comments:N/A