Summary of Study ST003398
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 PR002104. The data can be accessed directly via it's Project DOI: 10.21228/M8NJ9Q 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 | ST003398 |
| Study Title | Specific activation of the integrated stress response (ISR) uncovers regulation of lipid droplet biogenesis |
| Study Type | Biology |
| Study Summary | U2OS cells were treated with Dimerizer-PERK for 0h,1h,2h,4h,8h and 24h. Lipidomics analysis using LC-MS was performed on these samples to understand the regulation of cellular lipidome upon ISR activation |
| Institute | Calico Life Sciences |
| Department | Department of Mass Spectrometry-Technology Lab |
| Laboratory | Metabolomics Lab |
| Last Name | Vu |
| First Name | Ngoc |
| Address | 1130 Veterans BLVD, South San Francisco, CA 94080 |
| ngoc@calicolabs.com | |
| Phone | 650-420-5430 |
| Submit Date | 2024-08-08 |
| Num Groups | 6 |
| Total Subjects | 18 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-09-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005577 | AN005578 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Scientific Accucore C30 (250 × 2.1mm, 2.6um, 150 Å) | Thermo Scientific Accucore C30 (250 × 2.1mm, 2.6um, 150 Å) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Log2(Top Peak Area) | Log2(Top Peak Area) |
MS:
| MS ID: | MS005302 |
| Analysis ID: | AN005577 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer settings were as follows: data-dependent acquisition (DDA) was performed with the following parameters: resolution = 140,000, AGC target = 3.00 × 106, maximum IT (ms) = 100, scan range = 200–2000. The MS2 parameters were as follows: resolution = 17,500, AGC target = 3.00 × 106, maximum IT (ms) = 150, loop count = 8, isolation window (m/z) = 1, (N)CE = 20, 30, 40; underfill ratio = 1.00%, Apex trigger(s) = 5–30, dynamic exclusion(s) = 15 s. Maven software was used for data processing (Seitzer, P., Bennett, B. & Melamud, E. MAVEN2: An Updated Open-Source Mass Spectrometry Exploration Platform. Metabolites 12, 684 (2022).) Analysis of the lipidomics and metabolomics data was performed using Calico Lipidomics and Metabolomics Analysis (clamanR) package (https://github.com/calico/claman) in R. Raw files were converted to the mxML format using ProteoWizard Ver 3 88. Compound identifications were detected and grouped using the OpenCLaM R package (https://github.com/calico/open_clam) and manually inspected using the MAVEN2 peak analysis program (https://github.com/eugenemel/maven) 85 with the criteria of a precursor ion tolerance of 10 ppm and a product ion tolerance of 20 ppm, comparing fragmentation and retention time to an in-house library generated from authentic standards for metabolomics, and in-house generated in-silico libraries for lipidomics (https://github.com/calico/CalicoLipidLibrary). Per feature, our software assigned a unique groupID in a numerical format. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005303 |
| Analysis ID: | AN005578 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer settings were as follows: data-dependent acquisition (DDA) was performed with the following parameters: resolution = 140,000, AGC target = 3.00 × 106, maximum IT (ms) = 100, scan range = 200–2000. The MS2 parameters were as follows: resolution = 17,500, AGC target = 3.00 × 106, maximum IT (ms) = 150, loop count = 8, isolation window (m/z) = 1, (N)CE = 20, 30, 40; underfill ratio = 1.00%, Apex trigger(s) = 5–30, dynamic exclusion(s) = 15 s. Maven software was used for data processing (Seitzer, P., Bennett, B. & Melamud, E. MAVEN2: An Updated Open-Source Mass Spectrometry Exploration Platform. Metabolites 12, 684 (2022).) Analysis of the lipidomics and metabolomics data was performed using Calico Lipidomics and Metabolomics Analysis (clamanR) package (https://github.com/calico/claman) in R. Raw files were converted to the mxML format using ProteoWizard Ver 3 88. Compound identifications were detected and grouped using the OpenCLaM R package (https://github.com/calico/open_clam) and manually inspected using the MAVEN2 peak analysis program (https://github.com/eugenemel/maven) 85 with the criteria of a precursor ion tolerance of 10 ppm and a product ion tolerance of 20 ppm, comparing fragmentation and retention time to an in-house library generated from authentic standards for metabolomics, and in-house generated in-silico libraries for lipidomics (https://github.com/calico/CalicoLipidLibrary). Per feature, our software assigned a unique groupID in a numerical format. |
| Ion Mode: | NEGATIVE |
