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:
Project:
| Project ID: | PR000686 |
| Project DOI: | doi: 10.21228/M80Q2W |
| Project Title: | Trace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics |
| Project Type: | Study from Single-Cell Metabolomics |
| Project Summary: | The goal of this study was to validate the performance of a custom-written software tool, called Trace, for finding molecular features from ultrasensitive metabolomics experiments using high-resolution mass spectrometry. The software uses a trained neural network model to extract molecular features. As model for validation, we performed MS profiling of single identified cells from early developing embryos of the South African clawed frog (Xenopus laevis) using a custom-built capillary electrophoresis electrospray ionization platform coupled to a quadrupole time-of-flight mass spectrometer. The MS dataset from these measurements was manually curated for molecular features, and the resulting list of molecular features were used to test the robustness and accuracy of Trace at predicting molecular features that were detected from the single cells. |
| 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 |
| Email: | nemes@umd.edu |
| Phone: | 301-405-0373 |
| Funding Source: | National Cancer Institute award no. 7R03CA211635 |
| Publications: | Trace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics |
Subject:
| Subject ID: | SU001067 |
| Subject Type: | Other |
| Subject Species: | Xenopus laevis |
| Taxonomy ID: | 8355 |
| Age Or Age Range: | Embryos were obtained from natural mating of frogs (Nasco) |
| Weight Or Weight Range: | Sexually mature male and female frogs |
| Gender: | Not applicable |
Factors:
Subject type: Other; Subject species: Xenopus laevis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Embryo Type |
|---|---|---|
| SA064534 | D11cellE3T3 | WT |
| SA064535 | D11cellE5T1 | WT |
| SA064536 | D11cellE3T2 | WT |
| SA064537 | D11cellE3T1 | WT |
| SA064538 | D11cellE2T1 | WT |
| SA064539 | D11cellE4T1 | WT |
| SA064540 | D11cellE1T1 | WT |
| SA064541 | D11cellE2T2 | WT |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO001061 |
| Collection Summary: | Cells were identified based on morphology, pigmentation, and location in the embryo in comparision to established cell-fate maps for 16-cell Xenopus laevis embryos. A portion of the identified D11 cell was microaspirated using a fabricated microcapillary. |
| Collection Protocol ID: | Liu 2018 Metabolomics Workbench Protocol.pdf |
| Sample Type: | Embryonic cells |
| Collection Method: | Microaspiration of cell content |
| Collection Frequency: | 1 collection per cell |
| Collection Duration: | 5 s for aspiration |
| Volumeoramount Collected: | Ca. 10 nL per aspiration |
| Storage Conditions: | -80℃ |
| Collection Tube Temp: | chilled on ice |
Treatment:
| Treatment ID: | TR001081 |
| Treatment Summary: | All protocols related to the handling and manipulation of animals were approved by the Institutional Animal Care and Use Committee (IACUC) of the George Washington University (Washington, DC) and the University of Maryland, College Park (College Park, MD). |
| Treatment Protocol ID: | IACUC #A311 (George Washington University) and IACUC #R-DEC-17-57 (University of Maryland, College Park) |
| Treatment Protocol Filename: | Liu 2018 Metabolomics Workbench Protocol.pdf |
| Treatment Protocol Comments: | Embryos were dejellied using 2% cystine solution, cultured in 100% Steinberg's solution (media), and used without further treatment. |
Sample Preparation:
| Sampleprep ID: | SP001074 |
| Sampleprep Summary: | Ca. 10 nL of cell content were aspirated from identified cells. The aspirated material was ejected into ~4 uL of aqueous mixture of 40% acetonitrile and 40% methanol to extract metabolites. |
| Sampleprep Protocol ID: | Cold aqueous acetonitrile-methanold extraction |
| Sampleprep Protocol Filename: | Liu 2018 Metabolomics Workbench Protocol.pdf |
| Processing Storage Conditions: | On ice |
| Extraction Method: | In cold aqueous mixture of 40% acetonitrile and 40% methanol. |
| Extract Storage: | -80℃ |
| Sample Resuspension: | None. The cells were stored in the extraction solution. The extract was not dried or processed further. |
| Subcellular Location: | Unknown |
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 |
MS:
| MS ID: | MS001561 |
| Analysis ID: | AN001686 |
| Instrument Name: | Bruker Impact HD |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | Ca. 100 degC |
| Capillary Voltage: | -1700 V |
| Dry Gas Flow: | 2 L/min |
| Dry Gas Temp: | 100 degC |
| Ion Source Temperature: | 100 degC |
| Mass Accuracy: | <10 ppm |
| Dataformat: | .d (Bruker) |
| Resolution Setting: | ~45000 FWHM |
| Scanning Cycle: | 2 Hz spectral |
| Scanning Range: | m/z 50-550 |
