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MB Sample ID: SA316606
| Local Sample ID: | flg22(1-1) |
| Subject ID: | SU003030 |
| Subject Type: | Plant |
| Subject Species: | Arabidopsis thaliana |
| Taxonomy ID: | 3702 |
| Age Or Age Range: | 4-5 weeks |
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Combined analysis:
| Analysis ID | AN004787 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890B |
| Column | Agilent DB5-MS (30m x 0.25mm, 0.25um) |
| MS Type | EI |
| MS instrument type | Single quadrupole |
| MS instrument name | Agilent 5977B |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH003618 |
| Chromatography Summary: | For each sample, a 20 µL aliquot of AWF was lyophilized to dryness and resuspended in 10 µL of 30 mg/mL methoxyamine hydrochloride (Sigma-Aldrich) in pyridine (Sigma-Aldrich). The resuspended sample was incubated at 37°C and shaken at 1800 rpm for 90 minutes. After adding 20 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA) with 1% trimethylchlorosilane (CovaChem), the sample was incubated at 37°C and shaken at 1800 rpm for 30 minutes. Each derivatized sample was injected with a 10:1 split into an Agilent 7890B GC system with a 30 m +10 m Duraguard x 0.25 mm x 0.25 μm DB-5MS+DG Agilent column. The oven temperature was kept at 60°C for 1 minute, then ramped to 300°C at a rate of 10°C/min and held at 300°C for 10 minutes. Analytes were detected with an Agilent 5977B MSD in EI mode scanning from 50 m/z to 600 m/z. Mass spectrum analysis, component identification and peak area quantification were performed with AMDIS (http://www.amdis.net/). To reduce erroneous identifications during automated feature identification, the FiehnLib library was used to create a custom library that included both identified compounds along with unidentified prominent peaks that were recorded as unknowns and designated by their respective retention times72. Statistics were performed with MetaboAnalyst73 and MetaboAnalystR74. An in house perl script was used to collate AMDIS-generated peak areas into an Excel spreadsheet. Peaks that were present in blank samples containing derivatization chemicals only were removed from the data set. Two to three technical replicates were analyzed for each sample and averaged to produce a single sample value. MetaboAnalyst settings were selected to replace missing values by 1/5 of the minimum positive value for each feature and normalize the peak areas of the features by the peak area of the internal ribitol standard in each respective sample. |
| Instrument Name: | Agilent 7890B |
| Column Name: | Agilent DB5-MS (30m x 0.25mm, 0.25um) |
| Column Temperature: | 60 ramped to 300 |
| Flow Gradient: | NA |
| Flow Rate: | .52 mL/min helium gas |
| Injection Temperature: | 250 |
| Internal Standard: | ribitol |
| Solvent A: | NA |
| Solvent B: | NA |
| Chromatography Type: | GC |
| Solvent C: | NA |
