Summary of Study ST002330
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 PR001494. The data can be accessed directly via it's Project DOI: 10.21228/M8MD91 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 | ST002330 |
| Study Title | Early-stage responses to Plasmodiophora brassicae at the metabolome levels in clubroot resistant and susceptible oilseed Brassica napus |
| Study Type | Timecourse experiment |
| Study Summary | A total of 36 samples comprised two types of genotypes [CR (5 individuals pooled in each biological replicate) and CS (5 individuals pooled in each biological replicate)], two treatments (inoculated and uninoculated) and three biological replicates generated from three independent experiments and collected at 1-, 4-, and 7–DPI were used to extract primary and secondary metabolites and analyse the differences among the treatments. |
| Institute | Trent University |
| Department | Biology |
| Laboratory | Emery Lab |
| Last Name | Kisiala |
| First Name | Anna |
| Address | 1600 West Bank Drive, Trent University |
| annakisiala@trentu.ca | |
| Phone | 7057481011 |
| Submit Date | 2022-10-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-11-16 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003801 | AN003802 | AN003803 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 RS | Thermo Dionex Ultimate 3000 RS | Thermo Dionex Ultimate 3000 RS |
| Column | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm,2.7um) | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm,2.7um) | Phenomonex Kinetex C18 (50 x 2.1mm,2.6um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | NEGATIVE |
| Units | normalized relative level | normalized relative level | normalized relative level |
MS:
| MS ID: | MS003543 |
| Analysis ID: | AN003801 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Orbitrap QExactive was operated with a heated electrospray ionization (HESI) probe in positive mode. Temperatures of the HESI-II auxiliary gas heater and capillary were 450 and 300 °C, respectively, and the spray voltage was 3.9 kV. Sheath, auxiliary, and sweep gases were operated at 30, 8, and 0 (arbitrary units), respectively, and the S-lens RF level was 60. Each sample was analyzed using a mass range of m/z 70−900, and data were acquired at 70,000 resolution, automatic gain control (AGC) target of 1e6, and maximum injection time (IT) of 100 ms. Additionally, the top 10 data-dependent acquisition experiments were performed for the mixed sample from each group (HILIC and C18) to obtain compound MS/MS spectra. Processing of all full scan and ddMS2 data was conducted using the Xcalibur 4.1 software. Metabolites were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and comparison of fragmentation patterns to MS/MS databases (METLIN, PubChem). Metabolite relative concentration was normalized based on the average recoveries of 13C5-oT and 2H7-BAR as the internal standards |
| Ion Mode: | POSITIVE |
| MS ID: | MS003544 |
| Analysis ID: | AN003802 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Orbitrap QExactive was operated with a heated electrospray ionization (HESI) probe in negative mode. Temperatures of the HESI-II auxiliary gas heater and capillary were 450 and 300 °C, respectively, and the spray voltage was 3.9 kV. Sheath, auxiliary, and sweep gases were operated at 30, 8, and 0 (arbitrary units), respectively, and the S-lens RF level was 60. Each sample was analyzed using a mass range of m/z 70−900, and data were acquired at 70,000 resolution, automatic gain control (AGC) target of 1e6, and maximum injection time (IT) of 100 ms. Additionally, the top 10 data-dependent acquisition experiments were performed for the mixed sample from each group (HILIC and C18) to obtain compound MS/MS spectra. Processing of all full scan and ddMS2 data was conducted using the Xcalibur 4.1 software. Metabolites were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and comparison of fragmentation patterns to MS/MS databases (METLIN, PubChem). Metabolite relative concentration was normalized based on the average recoveries of 13C5-oT and 2H7-BAR as the internal standards |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003545 |
| Analysis ID: | AN003803 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Orbitrap QExactive was operated with a heated electrospray ionization (HESI) probe in negative mode. Temperatures of the HESI-II auxiliary gas heater and capillary were 450 and 300 °C, respectively, and the spray voltage was 3.9 kV. Sheath, auxiliary, and sweep gases were operated at 30, 8, and 0 (arbitrary units), respectively, and the S-lens RF level was 60. Each sample was analyzed using a mass range of m/z 70−900, and data were acquired at 70,000 resolution, automatic gain control (AGC) target of 1e6, and maximum injection time (IT) of 100 ms. Additionally, the top 10 data-dependent acquisition experiments were performed for the mixed sample from each group (HILIC and C18) to obtain compound MS/MS spectra. Processing of all full scan and ddMS2 data was conducted using the Xcalibur 4.1 software. Metabolites were identified by accurate mass, comparison of retention times to authentic standards or by accurate mass and comparison of fragmentation patterns to MS/MS databases (METLIN, PubChem). Metabolite relative concentration was normalized based on the average recoveries of 13C5-oT and 2H7-BAR as the internal standards |
| Ion Mode: | NEGATIVE |
