Return to study ST001489 main page
MB Sample ID: SA125447
| Local Sample ID: | 50_ |
| Subject ID: | SU001563 |
| Subject Type: | Plant |
| Subject Species: | Zea mays |
| Taxonomy ID: | 4577 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN002466 | AN002467 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) | ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak intensity | peak intensity |
MS:
| MS ID: | MS002286 |
| Analysis ID: | AN002466 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The raw acquisition data were processed using a similar workflow described in previous work (Chamberlain et al., 2019a, b), which we detail here. Raw data files were converted from .raw to .mzxml format using RawConverter (He et al., 2015). MZmine 2 was used for processing the raw data including detecting masses, building chromatograms, grouping isotopic peaks, removing duplicate peaks, and aligning features (Pluskal et al., 2010). Identification was assigned to features by m/z (≤5 ppm) and retention time (0.2 min) (level 1 – identified compounds according to Metabolomics Standards Initiative standards (Sumner et al., 2007)) matching tousing our method-specific metabolite library produced from pure standards previously analyzed using this the above-mentioned chromatographic gradient. Processed data were exported from MZmine as a feature list containing the signal intensity for each feature in each sample. A small value (half the minimum value in the dataset) was used to replace zeros (no detection). The data were filtered to remove sample features with 10% signal contribution from their corresponding features in the extraction blanks. From this point, the data were further processed, normalized, and filtered using MetaboAnalyst 4.0 (Chong et al., 2018). For whole-metabolome comparative analyses, the data were normalized to total ion signal and feature intensities were auto-scaled to facilitate statistical comparisons (van den Berg et al., 2006). Statistical significance, defined as p 0.05, was determined using the two-tailed student’s t-test, and values for significance were adjusted for the false discovery rate with the Bonferroni-Holm method (HOLM, 1979). |
| Ion Mode: | POSITIVE |
| MS ID: | MS002287 |
| Analysis ID: | AN002467 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The raw acquisition data were processed using a similar workflow described in previous work (Chamberlain et al., 2019a, b), which we detail here. Raw data files were converted from .raw to .mzxml format using RawConverter (He et al., 2015). MZmine 2 was used for processing the raw data including detecting masses, building chromatograms, grouping isotopic peaks, removing duplicate peaks, and aligning features (Pluskal et al., 2010). Identification was assigned to features by m/z (≤5 ppm) and retention time (0.2 min) (level 1 – identified compounds according to Metabolomics Standards Initiative standards (Sumner et al., 2007)) matching tousing our method-specific metabolite library produced from pure standards previously analyzed using this the above-mentioned chromatographic gradient. Processed data were exported from MZmine as a feature list containing the signal intensity for each feature in each sample. A small value (half the minimum value in the dataset) was used to replace zeros (no detection). The data were filtered to remove sample features with 10% signal contribution from their corresponding features in the extraction blanks. From this point, the data were further processed, normalized, and filtered using MetaboAnalyst 4.0 (Chong et al., 2018). For whole-metabolome comparative analyses, the data were normalized to total ion signal and feature intensities were auto-scaled to facilitate statistical comparisons (van den Berg et al., 2006). Statistical significance, defined as p 0.05, was determined using the two-tailed student’s t-test, and values for significance were adjusted for the false discovery rate with the Bonferroni-Holm method (HOLM, 1979). |
| Ion Mode: | NEGATIVE |
