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 |
|---|---|---|---|---|
| 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) |
MS:
| MS ID: | MS004598 |
| Analysis ID: | AN004853 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Set parameters on MS1 were 140,000 resolution, AGC target of 3e6 at max. IT of 100 ms with scan range of 200 to 2000 m/z. MS2 parameters consisted of 17,500 resolution at loop count 8, an AGC target of 3e6 at max. IT of 150 ms with isolation window set to 1 m/z and underfill ratio at 1%. Dynamic exclusion was set at 15 sec with an apex trigger from 5 to 30 sec. Stepped collision energies were set to 20, 30 and 40% NCE. Raw files were converted to mzML using MsConverter, and search against in-house libraries for feature identification using Maven 2. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004599 |
| Analysis ID: | AN004854 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Set parameters on MS1 were 140,000 resolution, AGC target of 3e6 at max. IT of 100 ms with scan range of 200 to 2000 m/z. MS2 parameters consisted of 17,500 resolution at loop count 8, an AGC target of 3e6 at max. IT of 150 ms with isolation window set to 1 m/z and underfill ratio at 1%. Dynamic exclusion was set at 15 sec with an apex trigger from 5 to 30 sec. Stepped collision energies were set to 20, 30 and 40% NCE. Raw files were converted to mzML using MsConverter, and search against in-house libraries for feature identification using Maven 2. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS004600 |
| Analysis ID: | AN004855 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer was operated in positive ion mode using data-dependent acquisition (DDA) mode with the following parameters: resolution = 70,000, AGC target = 3.00E + 06, maximum IT (ms) = 100, scan range = 70–1050. The MS2 parameters were as follows: resolution = 17,500, AGC target = 1.00E + 05, maximum IT (ms) = 50, loop count = 6, isolation window (m/z) = 1, (N)CE = 20, 40, 80; underfill ratio = 1.00%, Apex trigger(s) = 3–10, dynamic exclusion(s) = 25 |
| Ion Mode: | POSITIVE |
| MS ID: | MS004601 |
| Analysis ID: | AN004856 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer was operated in negative ion mode using data-dependent acquisition (DDA) mode with the following parameters: resolution = 70,000, AGC target = 1.00E + 06, maximum IT (ms) = 100, scan range = 70–1050. The MS2 parameters were as follows: resolution = 17,500, AGC target = 1.00E + 05, maximum IT (ms) = 50, loop count = 6, isolation window (m/z) = 1, (N)CE = 20, 50, 100; underfill ratio = 1.0 0%, Apex trigger(s) = 3–12, dynamic exclusion(s) = 20 |
| Ion Mode: | NEGATIVE |
