Summary of Study ST001028
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 PR000686. The data can be accessed directly via it's Project DOI: 10.21228/M80Q2W 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 | ST001028 |
| Study Title | Metabolic profiling of identified single cells in Xenopus laevis embryos |
| Study Type | Metabolic profiling of single cells |
| Study Summary | Single D11 cells were identified in 16-cell embryos of Xenopus laevis. Metabolites were extracted, and the extracts were analyzed using a custom-built capillary electrophoresis electrospray ionization platform coupled to a quadrupole time-of-flight mass spectrometer. The resulting metadata was analyzed by Trace, a custom-design software, designed to extract molecular feautres from trace-sensitive metabolomics experiments. The results were validated against molecular features that were extracted by manual curation of the same raw mass spectrometer files. |
| Institute | University of Maryland |
| Department | Department of Chemistry & Biochemistry |
| Laboratory | Nemes Laboratory |
| Last Name | Nemes |
| First Name | Peter |
| Address | 0107 Chemistry Building, 8051 Regents Dr, College Park, MD 20742 |
| nemes@umd.edu | |
| Phone | 3014050373 |
| Submit Date | 2018-07-25 |
| Num Groups | 5 biological replicates (different cells from different embryos) + 1-to-3 technical replicates (same extract analyzed multiple times) |
| Total Subjects | 5 different D11 cells were analyzed, each from a different embryo |
| Publications | Trace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-09-23 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN001686 |
|---|---|
| Analysis type | MS |
| Chromatography type | CE |
| Chromatography system | Custom built CE system |
| Column | Bare fused silica capillary |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker Impact HD |
| Ion Mode | POSITIVE |
| Units | PeakAreaInCounts |
Chromatography:
| Chromatography ID: | CH001186 |
| Chromatography Summary: | About 10 nL of metabolite extract were injected into bare fused silica capillary filled with the background electrolyte, then potential difference was applied between the capillary ends to electrophoretically separate metabolites. |
| Instrument Name: | Custom built CE system |
| Column Name: | Bare fused silica capillary |
| Column Temperature: | Room temperature (~21 degC) |
| Flow Rate: | Electroosmoti flow rates apply in this study (~1 nL/min, estimated) |
| Injection Temperature: | Room temperature (~21 degC) |
| Retention Time: | Metabolites were separated across ~45 min. |
| Sample Injection: | 10 nL |
| Solvent A: | 100% water; 1% formic acid |
| Capillary Voltage: | Ca. +20,000 V applied to inlet end of the CE fused silica separation capillary |
| Migration Time: | Ca. 45 min total run time collected |
| Preconditioning: | Sodium hydroxide solution |
| Running Buffer: | See background electrolyte (above) |
| Sheath Liquid: | 50% methanol, 0.1% formic acid |
| Chromatography Type: | CE |
