Summary of Study ST001032
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 PR000690. The data can be accessed directly via it's Project DOI: 10.21228/M8GQ3M This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001032 |
| Study Title | Single-cell Profiling of Cationic and Anionic Metabolites in Live Frog (Xenopus) Embryos using Microprobe Capillary Electrophoresis Mass Spectrometry |
| Study Type | Metabolic profiling of single cells |
| Study Summary | The goal of this study was to enable the analysis of anionic and cationic metabolites from the same identified single cell in Xenopus laevis embryos. A 10 nL portion of identified animal-ventral (V1) cells was aspirated from 8-cell embryos, and metabolites were extracted from the aspirate, before characterization of cationic and anionic compounds using a custom-built capillary electrophoresis (CE) electrospray ionization (ESI) mass spectrometry platform. A total of ~250 cationic molecular features and ~150 anionic molecular features were detected, including 76 metabolites that were identified in this study. Pathway analysis of the identified metabolites highlighted arginine-proline metabolism of significance. |
| Institute | University of Maryland |
| Department | Department of Chemistry & Biochemistry |
| Laboratory | Nemes Laboratory |
| Last Name | Nemes |
| First Name | Peter |
| Address | 0107 Chemistry Building 8051 Regents Drive |
| nemes@umd.edu | |
| Phone | 3014050373 |
| Submit Date | 2018-08-08 |
| Num Groups | 4 biological replicates (each different cell from a different embryo) + 1-to-2 technical replicates (same extract analyzed multiple times) |
| Total Subjects | 4 different V1 cells were analyzed, each from a different embryo |
| 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: | PR000690 |
| Project DOI: | doi: 10.21228/M8GQ3M |
| Project Title: | Single-cell Profiling of Cationic and Anionic Metabolites in Live Frog (Xenopus) Embryos using Microprobe Capillary Electrophoresis Mass Spectrometry |
| Project Type: | Metabolic profiling of anionic and cationic metabolites in single cells |
| Project Summary: | The goal of this study was to enable the analysis of anionic and cationic metabolites from the same identified single cell in Xenopus laevis embryos. A 10 nL portion of identified animal-ventral (V1) cells was aspirated from 8-cell embryos, and metabolites were extracted from the aspirate, before characterization of cationic and anionic compounds using a custom-built capillary electrophoresis (CE) electrospray ionization (ESI) mass spectrometry platform. A total of ~250 cationic molecular features and ~150 anionic molecular features were detected, including 76 metabolites that were identified in this study. Pathway analysis of the identified metabolites highlighted arginine-proline metabolism of significance. |
| 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 grant 7R03CA211635 |
Subject:
| Subject ID: | SU001071 |
| 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 |
| Species Group: | Mammals |
Factors:
Subject type: Other; Subject species: Xenopus laevis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Embryo Type |
|---|---|---|
| SA069156 | V1E3T2P | WT |
| SA069157 | V1E4T1N | WT |
| SA069158 | V1E3T1P | WT |
| SA069159 | V1E2T1N | WT |
| SA069160 | V1E2T1P | WT |
| SA069161 | V1E1T1N | WT |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO001065 |
| Collection Summary: | Cells were identified based on morphology, pigmentation, and location in the embryo in comparison to established cell-fate maps for Xenopus laevis embryos. A portion of the identified V1 cell was microaspirated using a fabricated microcapillary. |
| Collection Protocol ID: | Portero 2018 Metabolomics Workbench Protocols FINAL 2018-08-08 |
| Collection Protocol Filename: | nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf |
| Sample Type: | embryonic cell |
| 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℃ |
Treatment:
| Treatment ID: | TR001085 |
| Treatment Summary: | All protocols related to the handling and manipulation of animals were approved by the University of Maryland, College Park (College Park, MD). Embryos were dejellied using 2% cystine solution, cultured in 100% Steinberg's solution (media), and used without further treatment. |
| Treatment Protocol ID: | IACUC # R-DEC-17-57 |
| Treatment Protocol Filename: | nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf |
Sample Preparation:
| Sampleprep ID: | SP001078 |
| 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 Filename: | nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf |
| Processing Method: | On ice, then extracts stored at -80 degC until analysis. |
| Processing Storage Conditions: | On ice |
| Extraction Method: | In cold aqueous mixture of 40% acetonitrile and 40% methanol. |
| Extract Enrichment: | none |
| Extract Cleanup: | none |
| Extract Storage: | -80℃ |
| Subcellular Location: | Unknown |
Combined analysis:
| Analysis ID | AN001692 | AN001693 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | CE | CE |
| Chromatography system | Custom-built CE system | Custom-built CE system |
| Column | Bare fused silica capillary | Bare fused silica capillary |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Bruker Impact HD | Bruker Impact HD |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH001191 |
| Chromatography Summary: | Metabolites were separated in a custom-built capillary electrophoresis (CE) system. |
| Instrument Name: | Custom-built CE system |
| Column Name: | Bare fused silica capillary |
| Column Temperature: | Room temperature |
| Injection Temperature: | Room temperature |
| Sample Injection: | Ca. 10 nL |
| Solvent A: | 100% water; 1% formic acid |
| Analytical Time: | 45 min of separation |
| Capillary Voltage: | During cationic separation, +19,000-20,000 V was applied on the inlet end of the CE capillary. |
| Preconditioning: | Sodium hydroxide solution |
| Sheath Liquid: | During cationic analysis, the electrospray sheath solution was 50% methanol with 0.1% formic acid. |
| Chromatography Type: | CE |
| Chromatography ID: | CH001192 |
| Chromatography Summary: | Metabolites were separated in a custom-built capillary electrophoresis (CE) system. |
| Instrument Name: | Custom-built CE system |
| Column Name: | Bare fused silica capillary |
| Column Temperature: | Room temperature |
| Injection Temperature: | Room temperature |
| Sample Injection: | Ca. 10 nL |
| Solvent A: | 100% water; 20 mM ammonium bicarbonate |
| Analytical Time: | 45 min of separation |
| Capillary Voltage: | During anionic, +19,000-20,000 V was applied on the inlet end of the CE capillary. |
| Preconditioning: | Sodium hydroxide solution |
| Sheath Liquid: | During cationic analysis, the electrospray sheath solution was 0.2 mM ammonium bicarbonate in 50% isopropanol. |
| Chromatography Type: | CE |
MS:
| MS ID: | MS001567 |
| Analysis ID: | AN001692 |
| Instrument Name: | Bruker Impact HD |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 100 degC |
| Capillary Voltage: | +1700 V during cationic analysis |
| Mass Accuracy: | <5 ppm |
| Dataformat: | mzML |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | mz 50-550 |
| MS ID: | MS001568 |
| Analysis ID: | AN001693 |
| Instrument Name: | Bruker Impact HD |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 150 degC |
| Capillary Voltage: | -2100 during anionic analysis |
| Mass Accuracy: | <5 ppm |
| Dataformat: | mzML |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | mz 50-550 |
