Summary of Study ST001634
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001045. The data can be accessed directly via it's Project DOI: 10.21228/M8MQ3V This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001634 |
| Study Title | A combinatorial action of GmMYB176 and bZIP controls isoflavonoid biosynthesis in soybean. |
| Study Summary | This study identified how the GmMYB176 protein complex affects the metabolome of soybean hairy roots using non-targeted high resolution mass spectrometry. |
| Institute | Agriculture and Agri-Food Canada |
| Last Name | Renaud |
| First Name | Justin |
| Address | 1391 Sandford Street, London, Ontario, N5V 4T3, Canada |
| justin.renaud@canada.ca | |
| Phone | 519-953-6698 |
| Submit Date | 2020-12-17 |
| Num Groups | 2 |
| Total Subjects | 10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-01-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN002670 | AN002671 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 | Agilent 1290 |
| Column | Agilent Zorbax RRHD EclipsePlus (50 x 2.1mm,1.8um) | Agilent Zorbax RRHD EclipsePlus (50 x 2.1mm,1.8um) |
| 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 area | peak area |
MS:
| MS ID: | MS002469 |
| Analysis ID: | AN002670 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Thermo.raw files were converted to .mzml format using Protewizard , with peak peaking filter applied. Features were detected using the XCMS package with the centWave method (ppm tolerance 3.0). The signal to noise threshold was set to 5, noise was set to 5×105 and pre-filter was set to five scans with a minimum 5,000 intensity. Retention time correction was conducted using the obiwarp method.. Grouping of features was set to those present in at least 0.1% of all samples (retention time deviation 5 s; m/z width, 0.015). The ‘fillPeaks’ function was used with default settings. Zero values were imputed by 2/3 the minimum peak area value of a specific feature across all samples. PCA plots were obtained by log transforming the imputed XCMS peak area values, and ‘pareto’ scaling in Rstudio. Volcano plots were also generated using the imputed XCMS peak area values. Compounds were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and also comparison of fragmentation patterns to MS/MS databases. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002470 |
| Analysis ID: | AN002671 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Thermo.raw files were converted to .mzml format using Protewizard , with peak peaking filter applied. Features were detected using the XCMS package with the centWave method (ppm tolerance 3.0). The signal to noise threshold was set to 5, noise was set to 5×105 and pre-filter was set to five scans with a minimum 5,000 intensity. Retention time correction was conducted using the obiwarp method.. Grouping of features was set to those present in at least 0.1% of all samples (retention time deviation 5 s; m/z width, 0.015). The ‘fillPeaks’ function was used with default settings. Zero values were imputed by 2/3 the minimum peak area value of a specific feature across all samples. PCA plots were obtained by log transforming the imputed XCMS peak area values, and ‘pareto’ scaling in Rstudio. Volcano plots were also generated using the imputed XCMS peak area values. Compounds were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and also comparison of fragmentation patterns to MS/MS databases. |
| Ion Mode: | NEGATIVE |
