Summary of Study ST001102

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 IDST001102
Study TitlePhysiological and metabolic response of crab megalopae and juveniles to ocean acidification (part-II)
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 Date2018-11-29
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2019-01-22
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:SU001146
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 Treatment Duration (days)
SA075065M5D7_24High High 30
SA075066M7C6_26High High 30
SA075067M5B2_1High High 30
SA075068M5B3_25High High 30
SA075069M12A1_28High High 31
SA075070M8B2_8High High 31
SA075071M8D2_29High High 31
SA075072M12A1_46High High 31
SA075073M7D6_30High High 31
SA075074M12B3_53High High 32
SA075075M7D5_54High High 32
SA075076M12D3_34High High 32
SA075077M7A5_42High High 33
SA075078M8C1_58High High 33
SA075079M12B4_59High High 33
SA075080M11C2_2High Low 30
SA075081M10C5_27High Low 30
SA075082M10D2_47High Low 31
SA075083M4B1_9High Low 31
SA075084M4D5_49High Low 31
SA075085M11A2_48High Low 31
SA075086M10B5_35High Low 32
SA075087M10A7_17High Low 32
SA075088M11A7_60High Low 32
SA075089M10A7_43High Low 32
SA075090M10D3_56High Low 32
SA075091M11D3_55High Low 32
SA075092M4D4_38High Low 33
SA075093M11B2_22High Low 33
SA075094M11B2_44High Low 33
SA075095M2B3_5Low High 30
SA075096M2C1_6Low High 30
SA075097M2B6_4Low High 30
SA075098M3A7_3Low High 30
SA075099M2C6_50Low High 31
SA075100M2A1_51Low High 31
SA075101M3D5_31Low High 31
SA075102M3A2_12Low High 31
SA075103M3B2_11Low High 31
SA075104M3C3_10Low High 31
SA075105M2B4_13Low High 31
SA075106M2B7_57Low High 32
SA075107M2C4_36Low High 32
SA075108M3D6_37Low High 32
SA075109M2A3_23Low High 33
SA075110M6A6_7Low Low 30
SA075111M1C1_16Low Low 31
SA075112M1C2_14Low Low 31
SA075113M6C3_52Low Low 31
SA075114M1C4_32Low Low 31
SA075115M6D2_33Low Low 31
SA075116M6B3_15Low Low 31
SA075117M1A1_19Low Low 32
SA075118M6A5_18Low Low 32
SA075119M1B2_20Low Low 32
SA075120M1C5_21Low Low 32
SA075121M6C2_40Low Low 33
SA075122M1D1_41Low Low 33
SA075123M6B6_45Low Low 33
SA075124M1D7_39Low Low 33
Showing results 1 to 60 of 60


Collection ID:CO001140
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:TR001160
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:SP001153
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.

Combined analysis:

Analysis ID AN001791 AN001792
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 Agilent 1290
Column Waters Acquity CSH C18 (100 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF
Units Peak Height Peak Height


Chromatography ID:CH001265
Instrument Name:Agilent 1290
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Pressure:500-1000bar
Column Temperature:65°C
Flow Rate:600µL/min
Sample Injection:1.67µL
Chromatography Type:Reversed phase


MS ID:MS001653
Analysis ID:AN001791
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS ID:MS001654
Analysis ID:AN001792
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF