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.

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Study IDST001028
Study TitleMetabolic profiling of identified single cells in Xenopus laevis embryos
Study TypeMetabolic profiling of single cells
Study SummarySingle 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
DepartmentDepartment of Chemistry & Biochemistry
LaboratoryNemes Laboratory
Last NameNemes
First NamePeter
Address0107 Chemistry Building, 8051 Regents Dr, College Park, MD 20742
Emailnemes@umd.edu
Phone3014050373
Submit Date2018-07-25
Num Groups5 biological replicates (different cells from different embryos) + 1-to-3 technical replicates (same extract analyzed multiple times)
Total Subjects5 different D11 cells were analyzed, each from a different embryo
PublicationsTrace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics
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/M80Q2W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA064534D11cellE3T3WT
SA064535D11cellE5T1WT
SA064536D11cellE3T2WT
SA064537D11cellE3T1WT
SA064538D11cellE2T1WT
SA064539D11cellE4T1WT
SA064540D11cellE1T1WT
SA064541D11cellE2T2WT
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
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