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.

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Study IDST001634
Study TitleA combinatorial action of GmMYB176 and bZIP controls isoflavonoid biosynthesis in soybean.
Study SummaryThis 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 NameRenaud
First NameJustin
Address1391 Sandford Street, London, Ontario, N5V 4T3, Canada
Emailjustin.renaud@canada.ca
Phone519-953-6698
Submit Date2020-12-17
Num Groups2
Total Subjects10
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2021-01-07
Release Version1
Justin Renaud Justin Renaud
https://dx.doi.org/10.21228/M8MQ3V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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 (2.1 × 50 mm, 1.8 µm) Agilent Zorbax RRHD EclipsePlus (2.1 × 50 mm, 1.8 µm)
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
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