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:
Sample Preparation:
| Sampleprep ID: | SP003075 |
| Sampleprep Summary: | This method is based on the protocol Matyash et al. 2008. (Matyash et al. 2008). Briefly, lipid standards mixture (volumes as described in results) were extracted by addition of 50% methanol (pre-cooled to -20°C), vortexed for 30 sec, and incubated on ice for 10 min. The same volume of room temperature MTBE was added, and the samples were vortexed on the max setting for 30 sec before centrifuging at 3000 x g for 5 min at 4°C for a complete phase-separation (Eppendorf R5010 centrifuge with swinging bucket rotor). The maximum volume of the upper organic phase was pipetted off by hand with a Hamilton glass syringe until the meniscus of the two phases was reached. The organic phase was then transferred to a new ice-cold glass sample vial. The remaining sample volume was subjected to a secondary extraction using MTBE or other chemicals described in the results section. Then, the second organic phase was removed, combining this volume with the first organic phase extraction. All sample transfers involving MTBE-containing solutions were performed with glass syringes rinsed twice with MTBE and MeOH, between preparation steps. Following both MTBE extractions, the lower aqueous phase extract was pipetted off with the necessary care not to pick up the remaining upper phase or disturb the protein pellet. The fraction was subsequently transferred into a separate ice-cold sample vial. The phase extracts were then evaporated to dryness under nitrogen flow at 4°C and stored at -80°C. |
| Sampleprep Protocol ID: | A00003888 |
| Sampleprep Protocol Filename: | NIH Guide for the Care and Use of Laboratory Animals |
| Processing Storage Conditions: | On ice |
