Return to study ST001934 main page
MB Sample ID: SA181863
| Local Sample ID: | Eh_stem_4 |
| Subject ID: | SU002012 |
| Subject Type: | Plant |
| Subject Species: | Equisetum arvense;Equisetum hyemale;Equisetum telmateia |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002012 |
| Subject Type: | Plant |
| Subject Species: | Equisetum arvense;Equisetum hyemale;Equisetum telmateia |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Eh_stem_4 | SA181863 | FL022286 | E. hyemale | Species |
| Eh_stem_4 | SA181863 | FL022286 | stem | Organ |
Collection:
| Collection ID: | CO002005 |
| Collection Summary: | E. arvense, E. hyemale and E. telmateia (voucher specimens deposited with the John G. Searle Herbarium of the Field Museum, Chicago, IL, USA) were maintained in a greenhouse under ambient lighting, with supplemental lighting from sodium- vapor lamps. The photosynthetically active radiation varied from 15 to 25 mol m-2 d-1. Temperatures ranged between 22 and 27 °C and the humidity was set to 70 ± 10 %. Five biological replicates (separate plants) were harvested at the same time of day for below-ground rhizomes and above-ground stems of vegetative shoots. Samples were snap-frozen in liquid nitrogen and freeze-dried (aerial parts for 5 days, rhizomes for 7 days). Lyophilized material was submerged in liquid nitrogen, homogenized using mortar and pestle. |
| Sample Type: | Tissue homogenate |
| Storage Conditions: | -80 °C |
Treatment:
| Treatment ID: | TR002024 |
| Treatment Summary: | No Treatment |
Sample Preparation:
| Sampleprep ID: | SP002018 |
| Sampleprep Summary: | Five biological replicates (separate plants) were harvested at the same time of day for below-ground rhizomes and above-ground stems of vegetative shoots. Samples were snap-frozen in liquid nitrogen and freeze-dried (aerial parts for 5 days, rhizomes for 7 days). Lyophilized material was submerged in liquid nitrogen, homogenized using mortar and pestle. |
| Extraction Method: | Frozen tissue homogenate (30 mg per sample) was transferred to a 2 ml reaction tube and extracted with 1 ml of 80 % aqueous methanol (containing 10 mg/l anthracene-9-carboxylic acid as internal standard) by vigorous shaking (VX-2500 multi-tube vortexer, VWR Scientific, South Plainfield, NY, USA) for 10 min and subsequent sonication for 20 min (FS30 ultrasonic cleaner, Fisher Scientific, Hampton, NY, USA). Following centrifugation for 10 min at 13,000 × g (5415 microfuge, Eppendorf, Enfield, CT, USA), the supernatant was filtered through 0.22 μm polypropylene syringe filter tips, and the flow-through collected in plastic inserts for 2 ml reaction vials. |
Combined analysis:
| Analysis ID | AN003144 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 HPLC |
| Column | HD Zorbax SB-Aq (100 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6530 QTOF |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH002326 |
| Instrument Name: | Agilent 1290 HPLC |
| Column Name: | HD Zorbax SB-Aq (100 x 2.1mm,1.8um) |
| Column Temperature: | 60 °C |
| Flow Gradient: | 5 % B to 10 % B at 5 min, 20 % B at 10 min, 80 % B at 35 min, 95 % B at 45 min |
| Flow Rate: | 0.6 ml/min |
| Internal Standard: | 10 mg/l Anthracene-9-carboxylic acid |
| Sample Injection: | 10 ul |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Target Sample Temperature: | Autosampler set to 4 °C |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002924 |
| Analysis ID: | AN003144 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | HPLC–QTOF–MS with electrospray ion source (positive ion mode) Raw data sets were opened in the Profinder B.06.00 build 6.0.0625.0 software package (Agilent Technologies, Santa Clara, CA, USA) and molecular feature elements (MFEs) obtained using the Batch Recursive Feature Extraction algorithm. Binning and alignment tolerances were set to 10 % + 20 s for the retention time and 10 ppm + 2 mDa for the mass accuracy, and 0.0025 m/z + 5.0 ppm for the isotope grouping space tolerance. Additional parameters that were considered for feature extraction were quasi-molecular ions and adducts ([M+H]+, [M+Na]+, [M+K]+, [M+NH4]+), dimers, neutral losses (H2O, H3PO4, C6H10O5 (glucose), C12H20O9 (rutinose), C12H20O10 (sophorose), C6H10O4 (rhamnose), and C5H8O4 (xylose)), absolute peak height ≥ 2000 counts, and occurrence required in a minimum of four of the five replicates of each sample type. These pre-processing steps generated 848 MFEs (849 including ISTD), and exported into an Excel spreadsheet. Additional exclusion criteria for MFEs were: relative standard deviation of mass accuracy > 5.0 ppm; percent relative standard deviation returned as ”NaN” (Not a Number) or an empty cell; an unacceptably close accurate mass and retention time (± 0.010 m/z and ± 0.02 min.; screened as duplicates); or if it was a fragment. This additional filtering returned 544 remaining MFEs. Peak areas of MFEs for each sample were normalized based on sample weight and the peak area of the internal standard (MFEs without a peak area were filled in with a nominal value of two). |
| Ion Mode: | POSITIVE |
| Source Temperature: | 325 °C |
| Dataformat: | .d |
| Nebulizer: | 2.4 bar |
