Summary of Study ST001154
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 PR000773. The data can be accessed directly via it's Project DOI: 10.21228/M8RT1C 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 | ST001154 |
| Study Title | A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the International Mouse Phenotyping Consortium |
| Study Summary | Untargeted and targeted metabolomics datasets were acquired for blood plasma samples of 30 mouse knockouts within the International Mouse Phenotyping Consortium (IMPC). http://www.mousephenotype.org/. West Coast Metabolomics Center at UC Davis (https://metabolomics.ucdavis.edu/) conducted the metabolomics analyses. |
| Institute | University of California, Davis |
| Department | Genome Center |
| Laboratory | West Coast Metabolomics Center |
| Last Name | Barupal |
| First Name | Dinesh |
| Address | 451 East Health Science Drive |
| dinkumar@ucdavis.edu | |
| Phone | 5309794354 |
| Submit Date | 2019-03-12 |
| Num Groups | 31 |
| Total Subjects | 220 |
| Num Males | 110 |
| Num Females | 110 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf, raw(Thermo), mzML |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2019-04-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN001941 | AN001942 | AN001943 | AN001944 | AN001945 | AN001946 | AN001947 |
|---|---|---|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS | MS | MS | MS |
| Chromatography type | GC | Reversed phase | Reversed phase | HILIC | HILIC | Reversed phase | Reversed phase |
| Chromatography system | Agilent 6890N | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) | Waters Acquity BEH C18 (100 x 2mm,1.7um) | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| MS Type | EI | ESI | ESI | ESI | ESI | ESI | ESI |
| MS instrument type | GC-TOF | Orbitrap | Orbitrap | Orbitrap | Orbitrap | Ion trap | Ion trap |
| MS instrument name | Leco Pegasus IV TOF | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | ABI Sciex 6500 QTrap | ABI Sciex 6500 QTrap |
| Ion Mode | NEGATIVE | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE | UNSPECIFIED | NEGATIVE |
| Units | normalized peak height | normalized peak height | normalized peak height | normalized peak height | normalized peak height | nM | nM |
Chromatography:
| Chromatography ID: | CH001408 |
| Instrument Name: | Agilent 6890N |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
| Chromatography ID: | CH001409 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Flow Gradient: | 0 min 85% (A); 0-2 min 70% (A); 2-2.5 min 52% (A); 2.5-11 min 18% (A); 11-11.5 min 1% (A); 11.5-12 min 1% (A); 12-12.1 min 85% (A); 12.1-15 min 85% (A) |
| Solvent A: | Pos mode:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate, Neg mode:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium acetate |
| Solvent B: | Pos mode:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate, Neg mode:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001410 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | 100% (B) for 2 min, 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min and isocratic until 16.75 min. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.125% formic acid; 10 mM ammonium formate |
| Solvent B: | 95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001411 |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | The 20 min gradient is: 0-0.5 min 10% B, 0.5-1 min 10-20% B, 1-1.5 min 20-22.5% B, 1.5-11 min 22.5-45% B, 11-12.5 min 45-95% B, 12.5-16 min 95% B, 16-16.5 min 95-10% B, 16.5-20 min 10% B |
| Flow Rate: | 400 µL/min |
| Solvent A: | 100% water; 0.1% formic acid; |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001412 |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | 16 min gradient is: 0-1 min 25-40% B, 1-2.5 min 40-42% B, 2.5-4.5 min 42-50% B, 4.5-10.5 min 50-65% B, 10.5-12.5 min 65-75% B, 12.5-14 min 75-85% B, 14-14.5 min 85-95% B, 14.5-15 min 95-25% B, 15-16 min 25% B. |
| Flow Rate: | 250 µL/min |
| Solvent A: | 100% water; 0.1% acetic acid |
| Solvent B: | 90% acetonitrile/10% isopropanol; 0.1% acetic acid |
| Chromatography Type: | Reversed phase |
