Summary of Study ST001166

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 IDST001166
Study TitlePhysiological and metabolic response of pteropods to ocean acidification (part IV)
Study SummaryThe objective of the study was to examine the physiological and metabolic response of pteropods to ocean acidification treatment. Four treatments were used:high pH, high DO (dissolved oxygen); high pH, low DO; low pH, high DO; low pH, low DO
DepartmentCB Division
Last NameNichols
First NameKrista
Address1315 East-West Highway Silver Spring, MD 20910
Submit Date2019-04-05
Num Groups4
Total Subjects60
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:SU001231
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
SA080628M3A2High High
SA080629M3B3High High
SA080630M13A7High High
SA080631M13C2High High
SA080632M13B5High High
SA080633M3D4High High
SA080634M13D4High High
SA080635M3A3High High
SA080636M7D6High High
SA080637M7C5High High
SA080638M7C2High High
SA080639M7B2High High
SA080640M7A6High High
SA080641M13A2High High
SA080642M3C1High High
SA080643M6C6High Low
SA080644M12A1High Low
SA080645M6A1High Low
SA080646M6A2High Low
SA080647M6D4High Low
SA080648M6B3High Low
SA080649M6B7High Low
SA080650M6C7High Low
SA080651M12B2High Low
SA080652M12A2High Low
SA080653M12B3High Low
SA080654M12C2High Low
SA080655M12D4High Low
SA080656M12C6High Low
SA080657M6D2High Low
SA080658M5C1Low High
SA080659M5D1Low High
SA080660M8B1Low High
SA080661M8D4Low High
SA080662M8D6Low High
SA080663M8C1Low High
SA080664M5B6Low High
SA080665M8A5Low High
SA080666M10A6Low High
SA080667M5A1Low High
SA080668M10C3Low High
SA080669M5B5Low High
SA080670M10B1Low High
SA080671M10B4Low High
SA080672M10D7Low High
SA080673M11A2Low Low
SA080674M4A3Low Low
SA080675M11A4Low Low
SA080676M11B2Low Low
SA080677M11D7Low Low
SA080678M11D3Low Low
SA080679M1A7Low Low
SA080680M1C5Low Low
SA080681M4C3Low Low
SA080682M4B6Low Low
SA080683M4D1Low Low
SA080684M4D7Low Low
SA080685M1C7Low Low
SA080686M1D6Low Low
SA080687M4A2Low Low
Showing results 1 to 60 of 60


Collection ID:CO001225
Collection Summary:After completing the required treatment time of 30-33 days, each crab was frozen at -80C and shipped to the West Coast Metabolomics Center.
Sample Type:Muscle Tissue


Treatment ID:TR001246
Treatment Summary:Four treatments were used:high pH, high DO (dissolved oxygen); high pH, low DO; low pH, high DO; low pH, low DO.

Sample Preparation:

Sampleprep ID:SP001239
Sampleprep Summary:Crabs were removed from -80°C. 15 mg of muscle tissue was removed from each crab and placed in a 2 mL eppendorph tube. 2 x 3mm grinding beads were added to each sample. 225 µL of methanol with quality control standards were added to each sample. Samples were ground for 30 seconds at 1500 rpm using a GenoGrinder. 750 µL of methyl-tertbutyl ether (MTBE) was added to each sample. Samples were vortexed for 10 seconds and then shaked at 4°C for 6 minutes. 188 µL of LC-MS grade water was added to each sample. Samples were vortexed for 10 seconds and then centrifuged for 2 minutes at 14,000 rcf. The top, organic layer was split into two 350 µL aliquots, one submitted to lipidomics analysis and one saved for backup. The bottom layer was split into two 125 µL aliquots, one submitted to GC analysis and one saved as a backup.

Combined analysis:

Analysis ID AN001928
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus HT TOF
Units Peak Height


Chromatography ID:CH001399
Instrument Name:Agilent 7890A
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Column Temperature:50-330
Flow Rate:1 mL/min
Injection Temperature:50°C ramped to 250°C by 12°C s-1
Sample Injection:0.5 uL
Oven Temperature:50°C for 1 min, then ramped at 20°C min-1 to 330°C, held constant for 5 min
Chromatography Type:GC


MS ID:MS001784
Analysis ID:AN001928
Instrument Name:Leco Pegasus HT TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:N/A
Ion Source Temperature:250°C
Ionization Energy:-70 eV
Dataformat:.peg, .txt, .cdf
Resolution Setting:17 spectra/sec
Scanning Range:80-500 Da