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 |
Chromatography:
| Chromatography ID: | CH003396 |
| Chromatography Summary: | A 2.5 µL of the metabolite extract was loaded onto a reversed-phase LC column featuring anion-exchange chemistry (Atlantis PREMIER BEH C18 AX Column, Waters, 1.7 µm, 2.1 × 100 mm) and separated at 500 uL/min in a micro-flow LC system (ACQUITY I-Class, Waters) using a gradient of buffer A (100% ACN) and buffer B (95% water, 5% ACN with 1 mM ammonium acetate; pH 7.8) as follows: 5% was held 0–¬0.5 min, then linearly increased to 90% over 9.5 min, and held at 90% for 3 min. To recover and recondition the analytical column before the next sample injection, solvent B was then decreased to 5% over 2 min and the column was rinsed for 7 min. The column temperature was set to 30 °C. |
| Methods Filename: | Baxi_2023_Organizer_Work_MeabolomicsWorkBench_Description_2023-07-02.docx |
| Instrument Name: | Waters ACQUITY I-Class |
| Column Name: | Waters Atlantis Premier BEH C18 AX (100 x 2.1mm, 1.7um) |
| Column Temperature: | 30 |
| Flow Gradient: | 5% B was held 0–0.5 min, then linearly increased to 90% over 9.5 min, and held at 90% for 3 min |
| Flow Rate: | 500 uL/min |
| Solvent A: | 100% ACN |
| Solvent B: | 95% water/5% acetonitrile; 1 mM ammonium acetate; pH 7.8 |
| Chromatography Type: | Ion exchange |
| Chromatography ID: | CH003397 |
| Chromatography Summary: | A 2.5 µL of the metabolite extract was loaded onto a reversed-phase LC column featuring anion-exchange chemistry (Atlantis PREMIER BEH C18 AX Column, Waters, 1.7 µm, 2.1 × 100 mm) and separated at 500 uL/min in a micro-flow LC system (ACQUITY I-Class, Waters) using a gradient of buffer A (100% ACN) and buffer B (95% water, 5% ACN with 1 mM ammonium acetate; pH 7.8) as follows: 5% was held 0–¬0.5 min, then linearly increased to 90% over 9.5 min, and held at 90% for 3 min. To recover and recondition the analytical column before the next sample injection, solvent B was then decreased to 5% over 2 min and the column was rinsed for 7 min. The column temperature was set to 30 °C. |
| Methods Filename: | Baxi_2023_Organizer_Work_MeabolomicsWorkBench_Description_2023-07-02.docx |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Atlantis Premier BEH C18 AX (100 x 2.1mm, 1.7um) |
| Column Temperature: | 30 |
| Flow Gradient: | 5% B was held 0–0.5 min, then linearly increased to 90% over 9.5 min, and held at 90% for 3 min |
| Flow Rate: | 500 uL/min |
| Solvent A: | 100% ACN |
| Solvent B: | 95% water/5% acetonitrile; 1 mM ammonium acetate; pH 7.8 |
| Chromatography Type: | Ion exchange |
| Chromatography ID: | CH003398 |
| Chromatography Summary: | A 2-µL volume of the metabolite extract was loaded onto an ACQUITY UPLC BEH amide column (130 A, 1.7 µm, 1 mm × 100 mm) and separated at 45 ℃ using a mobile phase delivered at 130 uL/min in a micro-LC system (Waters ACQUITY I-Class). The separation was performed in buffer A (water containing 0.1% v/v FA) with a gradient of buffer B (100% ACN with 0.1% v/v FA) as follows: 1% A for 0.05 min, then ramped to 80% A over 3.20 min, held at 80% A for 2 min, ramped to 1% A in 1.75 min. To recover and condition the analytical column for the next sample injection, buffer A was held at 1% for 7 min. |
| Methods Filename: | Baxi_2023_Organizer_Work_MeabolomicsWorkBench_Description_2023-07-02.docx |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | ACQUITY UPLC BEH amide (100 x 1mm, 1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | 1% A for 0.05 min, then ramped to 80% A over 3.20 min, held at 80% A for 2 min, ramped to 1% A in 1.75 min |
| Flow Rate: | 130 uL/min |
| Solvent A: | water containing 0.1% v/v FA |
| Solvent B: | 100% acetonitrile; 0.1% v/v FA |
| Chromatography Type: | HILIC |
