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.

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Study IDST001032
Study TitleSingle-cell Profiling of Cationic and Anionic Metabolites in Live Frog (Xenopus) Embryos using Microprobe Capillary Electrophoresis Mass Spectrometry
Study TypeMetabolic profiling of single cells
Study SummaryThe 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
DepartmentDepartment of Chemistry & Biochemistry
LaboratoryNemes Laboratory
Last NameNemes
First NamePeter
Address0107 Chemistry Building 8051 Regents Drive
Emailnemes@umd.edu
Phone3014050373
Submit Date2018-08-08
Num Groups4 biological replicates (each different cell from a different embryo) + 1-to-2 technical replicates (same extract analyzed multiple times)
Total Subjects4 different V1 cells were analyzed, each from a different embryo
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2019-09-23
Release Version1
Peter Nemes Peter Nemes
https://dx.doi.org/10.21228/M8GQ3M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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

Factors:

Subject type: Other; Subject species: Xenopus laevis (Factor headings shown in green)

mb_sample_id local_sample_id Embryo Type
SA069156V1E3T2PWT
SA069157V1E4T1NWT
SA069158V1E3T1PWT
SA069159V1E2T1NWT
SA069160V1E2T1PWT
SA069161V1E1T1NWT
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:During cationic separation, the background electrolyte used in postive ionization mode was 1% formic acid in water (isocratic).
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:During anionic separation, the background electrolyte used in postive ionization mode was 20 mM ammonium bicarbonate (isocratic).
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
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