Summary of Study ST002778
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 PR001733. The data can be accessed directly via it's Project DOI: 10.21228/M8PX3J 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 | ST002778 |
| Study Title | Cell Lineage-Guided Microanalytical Mass Spectrometry Reveals Increased Energy Metabolism and Reactive Oxygen Species in the Vertebrate Organizer |
| Study Summary | We performed targeted metabolomic analysis on the Spemann-Mangold Organizer (SMO) tissue in the frog (Xenopus laevis) and the remainder of dissected embryos (RE). Metabolites were extracted from the dissected tissues, reconstituted, and analyzed using liquid chromatography (LC) electrospray ionization (ESI) mass spectrometry (MS). The targeted metabolite measurements were performed on a trapped ion mobility time-of-flight mass spectrometer (timsTOF PRO, Bruker). |
| Institute | University of Maryland |
| Department | Chemistry & Biochemistry |
| Last Name | Nemes |
| First Name | Peter |
| Address | 8051 Regents Drive, College Park, MD 20742, USA |
| nemes@umd.edu | |
| Phone | 3014050373 |
| Submit Date | 2023-07-03 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-01-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004522 | AN004523 | AN004524 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | Ion exchange | Ion exchange | HILIC |
| Chromatography system | Waters ACQUITY I-Class | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | Waters Atlantis Premier BEH C18 AX (100 x 2.1mm, 1.7um) | Waters Atlantis Premier BEH C18 AX (100 x 2.1mm, 1.7um) | ACQUITY UPLC BEH amide (100 x 1mm, 1.7um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | QTOF | QTOF | QTOF |
| MS instrument name | Bruker timsTOF PRO | Bruker timsTOF PRO | Bruker timsTOF PRO |
| Ion Mode | NEGATIVE | NEGATIVE | POSITIVE |
| Units | Counts | Counts | Counts |
MS:
| MS ID: | MS004269 |
| Analysis ID: | AN004522 |
| Instrument Name: | Bruker timsTOF PRO |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The metabolites were ionized in a micro-flow electrospray source equipped with an ionBooster-ESI device with the following settings: end plate, 400 V; capillary voltage, 1,000 V; charge voltage, 300 V; vaporizer temperature, 240 °C; sheath gas, 1.5 L/min; nebulizer, 4.1 bar; dry gas, 2.6 L/min; dry temperature, 200 °C. The ions were detected in the negative ionization mode using the following settings: survey (MS1) low- and middle-mass range, m/z 20–300 and m/z 50–1,300, respectively; spectral acquisition rate, 2 Hz. A list of metabolite ions was targeted using multiple reaction monitoring. Ions were isolated with 4-Da window (± 2 Da) for collision-induced dissociation (CID). The low-mass range (m/z 20–300) employed the following optimization for collision energy and m/z tuning: 12 eV at 115.0026; 12 eV at 145.0132; 12 eV at 168.9897; 12 eV at 184.9846; 10 eV at 191.0186. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | Baxi_2023_Organizer_Work_MeabolomicsWorkBench_Description_2023-07-02.docx |
| MS ID: | MS004270 |
| Analysis ID: | AN004523 |
| Instrument Name: | Bruker timsTOF PRO |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The metabolites were ionized in a micro-flow electrospray source equipped with an ionBooster-ESI device with the following settings: end plate, 400 V; capillary voltage, 1,000 V; charge voltage, 300 V; vaporizer temperature, 240 °C; sheath gas, 1.5 L/min; nebulizer, 4.1 bar; dry gas, 2.6 L/min; dry temperature, 200 °C. The ions were detected in the negative ionization mode using the following settings: survey (MS1) low- and middle-mass range, m/z 20–300 and m/z 50–1,300, respectively; spectral acquisition rate, 2 Hz. A list of metabolite ions was targeted using multiple reaction monitoring. Ions were isolated with 4-Da window (± 2 Da) for collision-induced dissociation (CID). The middle-mass range (m/z 50–1,300) employed the following optimization for collision energy and m/z tuning: 15 eV at 338.9877; 18 eV at 346.0553; 25 eV at 426.0216; 20 eV at 505.9879. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | Baxi_2023_Organizer_Work_MeabolomicsWorkBench_Description_2023-07-02.docx |
| MS ID: | MS004271 |
| Analysis ID: | AN004524 |
| Instrument Name: | Bruker timsTOF PRO |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The GSH and GSSG ion signals were measured in the positive ion mode and detected on the timsTOF PRO (Bruker) mass spectrometer with the following parameters: mass range, m/z 100–800; spectral acquisition rate, 4 Hz; scan mode, MRM (GSH: m/z 308.0911, charge state +1, retention time 2.5 min, width 4 Da (+/– 2 Da), and collision energy 26 eV); and GSSG (m/z 307.0833, charge state +2, retention time 2.9 min, width 4 Da (+/– 2 Da), collision energy 20 eV). |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Baxi_2023_Organizer_Work_MeabolomicsWorkBench_Description_2023-07-02.docx |
