Summary of Study ST002012

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 PR001276. The data can be accessed directly via it's Project DOI: 10.21228/M8S70F This work is supported by NIH grant, U2C- DK119886.


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Study IDST002012
Study TitleUntargeted primary metabolite profiling in Arabidopsis thaliana
Study SummaryThe goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.
Salk Institute for Biological Studies
LaboratoryJoanne Chory
Last NameWu
First NameXuelin
AddressSalk Institute for Biological Studies
Phone858-453-4100, x1128
Submit Date2021-12-09
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2022-01-02
Release Version1
Xuelin Wu Xuelin Wu application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001276
Project DOI:doi: 10.21228/M8S70F
Project Title:Untargeted primary metabolite profiling in Arabidopsis thaliana
Project Summary:The goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.
Institute:Salk Institute for Biological Studies
Laboratory:Joanne Chory
Last Name:Wu
First Name:Xuelin
Address:Salk Institute for Biological Studies
Funding Source:HHMI, TED Audacious Project


Subject ID:SU002098
Subject Type:Plant
Subject Species:Arabidopsis thaliana
Taxonomy ID:3702


Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)

mb_sample_id local_sample_id organ genotype
SA1889858_008inflourescences 12-6_F
SA1889867_007inflourescences 12-6_F
SA1889879_009inflourescences 12-6_F
SA18898810_010inflourescences 12-6_F
SA18898911_011inflourescences 12-6_F
SA18899012_012inflourescences 12-6_F
SA18899130_030inflourescences 18-4_F
SA18899228_028inflourescences 18-4_F
SA18899325_025inflourescences 18-4_F
SA18899426_026inflourescences 18-4_F
SA18899527_027inflourescences 18-4_F
SA18899629_029inflourescences 18-4_F
SA18899748_048inflourescences 290_F
SA18899843_043inflourescences 290_F
SA18899944_044inflourescences 290_F
SA18900045_045inflourescences 290_F
SA18900146_046inflourescences 290_F
SA18900247_047inflourescences 290_F
SA18900362_062inflourescences Col-0_F
SA18900465_065inflourescences Col-0_F
SA18900566_066inflourescences Col-0_F
SA18900663_063inflourescences Col-0_F
SA18900764_064inflourescences Col-0_F
SA18900861_061inflourescences Col-0_F
SA18900917_017leaves 12-6_L
SA18901016_016leaves 12-6_L
SA18901118_018leaves 12-6_L
SA18901215_015leaves 12-6_L
SA18901313_013leaves 12-6_L
SA18901414_014leaves 12-6_L
SA18901535_035leaves 18-4_L
SA18901636_036leaves 18-4_L
SA18901734_034leaves 18-4_L
SA18901833_033leaves 18-4_L
SA18901931_031leaves 18-4_L
SA18902032_032leaves 18-4_L
SA18902154_054leaves 290_L
SA18902253_053leaves 290_L
SA18902349_049leaves 290_L
SA18902452_052leaves 290_L
SA18902550_050leaves 290_L
SA18902651_051leaves 290_L
SA18902771_071leaves Col-0_L
SA18902872_072leaves Col-0_L
SA18902970_070leaves Col-0_L
SA18903069_069leaves Col-0_L
SA18903167_067leaves Col-0_L
SA18903268_068leaves Col-0_L
SA1890334_004roots 12-6_R
SA1890346_006roots 12-6_R
SA1890355_005roots 12-6_R
SA1890363_003roots 12-6_R
SA1890372_002roots 12-6_R
SA1890381_001roots 12-6_R
SA18903923_023roots 18-4_R
SA18904020_020roots 18-4_R
SA18904124_024roots 18-4_R
SA18904219_019roots 18-4_R
SA18904322_022roots 18-4_R
SA18904421_021roots 18-4_R
SA18904542_042roots 290_R
SA18904641_041roots 290_R
SA18904738_038roots 290_R
SA18904840_040roots 290_R
SA18904937_037roots 290_R
SA18905039_039roots 290_R
SA18905159_059roots Col-0_R
SA18905260_060roots Col-0_R
SA18905357_057roots Col-0_R
SA18905455_055roots Col-0_R
SA18905556_056roots Col-0_R
SA18905658_058roots Col-0_R
Showing results 1 to 72 of 72


Collection ID:CO002091
Collection Summary:Samples were collected from live plants and frozen in liquid nitrogen
Sample Type:Plant


Treatment ID:TR002110
Treatment Summary:four genotypes, each with three tissue types, 6, no treatment, just genotype and tissue type difference.

Sample Preparation:

Sampleprep ID:SP002104
Sampleprep Summary:Extraction of Plant Samples: Leaves 1. References: Fiehn O (2006) Metabolite Profiling in Arabidopsis. In: Arabidopsis Protocols 2nd edition. Salinas J, Sanchez-Serrano JJ (eds.), Methods in Molecular Biology ser., Humana Press, Totowa NJ, 439-447 Weckwerth W, Wenzel K, Fiehn O (2004) Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4, 78-83 2. Starting material: Arabidopsis rosette leaves: 20±5 mg fresh weight sample OR 2 mg dry weight sample Rice leaves: 10±3 mg fresh weight sample OR 1 mg dry weight sample Other plant organs not validated but advised to use this SOP in a similar manner 3. Equipment: Eppendorf pipettes: 1-200µL and 100-1000µL Eppendorf tubes 2.0mL, uncoloured (Cat. No. 022363204 ) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Precision balance with accuracy ± 0.1 mg ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer, VWR. Speed vacuum concentration system (Labconco Centrivap cold trap) Ball mill MM301 (Retsch corp.) Metal balls (Retsch 3 mm I.D. Cat. No 22.455.0002 or 5 mm I.D. Cat. No 22.455.0003) Large tweezers Dewar cold gloves 2 liquid nitrogen dewars pH paper 5-10 (EMD Chem. Inc.) Crushed ice Nitrogen line with pipette tip Cork borer (Ø diameter of cylinder related to the amount to be used. 4 mm I.D. for Arabidopsis leaves.) 4. Chemicals Methanol, LCMS grade Chloroform, HPLC grade Liquid nitrogen Water, Millipore (pure) 5. Harvest Procedure NOTE: No weighing of plant material needed unless the experimental design suggests marked changes for the ratio of leaf disk diameter to fresh weight, e.g. in drought stress experiments. In such cases, leaves need to be lyophilized and weighed prior to extraction Label Eppendorf tubes according to the sample name defined in SetupX and put a grinding ball in each. Using the cork borer take one or two disks per leaf and immediately transfer to an Eppendorf tube. Close the tube and immediately place into the dewar of liquid nitrogen. 6. Preparation of extraction mix and material Check the pH of methanol (pH7) Switch on the ThermoElectron Neslab RTE 740 cooling bath at to pre-cool at –18°C to -22°C Make the extraction solution by mixing methanol, chloroform, and water in proportions of 5 : 2 : 2 Rinse the extraction solution for 5 min with nitrogen, making sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution. 7. Homogenisation and extraction Take the Eppendorf tubes from the liquid nitrogen and place into the tube-holder of the grinder being careful to compensate for weight, maintaining equilibrium. Shake for 30s at a frequency of 25 s-1 and check that the leaves have been ground into a fine powder. Repeat if necessary, submerging in liquid nitrogen first. After grinding add 1mL of pre-chilled extraction solution to each tube one by one to prevent even partial thawing of the sample. Store all samples on ice while finishing this step. Vortex the sample for 10s and shake on the Orbital Mixing Chilling/Heating Plate for 6 minutes at 4°C Centrifuge for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. Remove the whole supernatant in two 500uL portions, saving one as a backup. Dry one portion in the Labconco Centrivap cold trap concentrator to complete dryness and submit for derivitization. 8. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 8. Quality assurance For each sequence perform one blank negative control by applying the total procedure (i.e. all materials and plastic ware) without biological sample. Also perform all tasks once samples/standards have come to room temperature. Finally, include a pure MSTFA vial for liner conditioning steps. 9. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules.

Combined analysis:

Analysis ID AN003286
Analysis type MS
Chromatography type GC
Chromatography system Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS
Column Rtx-5Sil MS
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Units normalized peak height


Chromatography ID:CH002426
Chromatography Summary:Gas Chromatography conditions: A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min.
Instrument Name:Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS
Column Name:Rtx-5Sil MS
Chromatography Type:GC


MS ID:MS003057
Analysis ID:AN003286
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:Mass spectrometer settings: A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da.