Summary of Study ST002956
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 PR001839. The data can be accessed directly via it's Project DOI: 10.21228/M80T6F 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 | ST002956 |
| Study Title | Automated preparation of plasma lipids, metabolites, and proteins for LC/MS-based analysis of a high-fat diet in mice |
| Study Type | Method Development |
| Study Summary | We designed an automated liquid-liquid extraction method with minimal contamination and human intervention. This approach enables accurate and precise collection of metabolite, lipid fractions, and protein pellet from a small volume of mice plasma for multiomic analysis. |
| Institute | Calico Life Sciences |
| Department | Department of Mass Spectrometry-Technology Lab |
| Laboratory | Metabolomics Lab |
| Last Name | Vu |
| First Name | Ngoc |
| Address | 1130 Veterans BLVD |
| ngoc@calicolabs.com | |
| Phone | 6504205430 |
| Submit Date | 2023-07-06 |
| Num Groups | 3 |
| Total Subjects | 90 |
| Num Males | 90 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-07-29 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004853 | AN004854 | AN004855 | AN004856 |
|---|---|---|---|---|
| Chromatography ID | CH003664 | CH003664 | CH003665 | CH003666 |
| MS ID | MS004598 | MS004599 | MS004600 | MS004601 |
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | Ion pair |
| Chromatography system | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C30 column (250 x 2.1 mm, 2.6 µm) | Thermo Accucore C30 column (250 x 2.1 mm, 2.6 µm) | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) | Agilent Zorbax Extend C18 column (150 x 2.1 mm, 1.8 µm) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Log2(Top Peak Area) | Log2(Top Peak Area) | Log2(Top Peak Area) | Log2(Top Peak Area) |
Chromatography:
| Chromatography ID: | CH003664 |
| Chromatography Summary: | RPLC method for lipidomics |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 column (250 x 2.1 mm, 2.6 µm) |
| Column Temperature: | 35 |
| Flow Gradient: | The column was equilibrated in 30% B for 7 minutes before injection. The gradient then increased to 43% B for another 7 minutes, followed by an increase to 65% B over 5 min and then slowly increasing to 70% B over 18 min. B was then increased to 88% for 1 min, followed by another slow increase to 95% over 20 min. Over the next 2 min, B was increased to 100%, followed by isocratic flow for another 2 min. After this step, the gradient was dropped to 30% B within 0.1 min and kept on isocratic flow for the next 5 min, resulting in a total run time of 67 min. |
| Flow Rate: | 200 uL/min |
| Solvent A: | 20 mM ammonium formate in [60:40] ACN:H2O, 0.25 µM medronic acid |
| Solvent B: | 20 mM ammonium formate in 90:10 IPA:MeCN, 0.25 µM medronic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003665 |
| Chromatography Summary: | HILIC method for Metabolomics |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 35 |
| Flow Gradient: | t = −6, 80% B; t = 0, 80% B; t = 2.5, 73% B; t = 5, 65% B, t = 7.5, 57% B; t = 10, 50% B; t = 15, 35% B; t = 20; 20% B; t = 22, 15% B; t = 22.5, 80% B; t = 24; 80% B. |
| Flow Rate: | 150uL/min |
| Solvent A: | 20 mM ammonium carbonate in water (pH 9.2) |
| Solvent B: | 100% MeCN |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003666 |
| Chromatography Summary: | RPLC method for Metabolomics |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Agilent Zorbax Extend C18 column (150 x 2.1 mm, 1.8 µm) |
| Column Temperature: | 30 |
| Flow Gradient: | The gradient eluted isocratically in 0% B for 2.5 min, increased to 20% B over 2.5 min, held at 20% B for 2.5 min, increased to 55% B over 5.5 min, increased to 95% B over 2.5 minutes, maintained at 95% B for 3 min, then decreased to 0% B over 0.5 min, where it was held for 3 min, resulting in a total run time of 26 min. |
| Flow Rate: | 200 uL/min |
| Solvent A: | 10 mM tributylamine and 15 mM acetic acid in [97:3] H2O:MeOH at pH 4.95 with 0.25 µM medronic acid |
| Solvent B: | 100% MeOH |
| Chromatography Type: | Ion pair |
