Summary of Study ST002890

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 PR001803. The data can be accessed directly via it's Project DOI: 10.21228/M8NQ7P 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 IDST002890
Study TitleCharacterization of the in vivo deuteration of native phospholipids by mass spectrometry yields guidelines for their regiospecific customization
Study SummaryCustomization of deuterated biomolecules is vital for many advanced biological experiments, including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating E. coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of thirty-six lipid species were quantitatively profiled in fifteen different growth conditions and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.
Institute
University of Tennessee
DepartmentGenome Science and Technology (Bredesen Center)
Last NameMatthew
First NameKeller
AddressThe Bredesen Center for Interdisciplinary Research and Graduate Education 444 Greve Hall, 821 Volunteer Blvd. Knoxville, TN 37996-3394
Emailqrh579@vols.utk.edu
Phone18659747999
Submit Date2023-09-26
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-10-12
Release Version1
Keller Matthew Keller Matthew
https://dx.doi.org/10.21228/M8NQ7P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001803
Project DOI:doi: 10.21228/M8NQ7P
Project Title:Characterization of the in vivo deuteration of native phospholipids by mass spectrometry yields guidelines for their regiospecific customization
Project Summary:Customization of deuterated biomolecules is vital for many advanced biological experiments, including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating E. coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of thirty-six lipid species were quantitatively profiled in fifteen different growth conditions and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.
Institute:University of Tennessee
Department:Genome Science and Technology (Bredesen Center)
Last Name:Matthew
First Name:Keller
Address:The Bredesen Center for Interdisciplinary Research and Graduate Education 444 Greve Hall, 821 Volunteer Blvd
Email:qrh579@vols.utk.edu
Phone:18659747999
Publications:In review at Analytical Chemistry
Contributors:Qiu Zhang, Shuo Qian, Brian Sanders, Hugh O'Neill, Robert Hettich

Subject:

Subject ID:SU003003
Subject Type:Bacteria
Subject Species:Escherichia coli
Genotype Strain:BL21(DE3)

Factors:

Subject type: Bacteria; Subject species: Escherichia coli (Factor headings shown in green)

mb_sample_id local_sample_id Carbon source Percent D2O MS ionization mode
SA315384H-Glu/25_2-neg50/50 H/D-Glycerol 0 negative
SA315385H-Glu/25_3-neg50/50 H/D-Glycerol 0 negative
SA315386H-Glu/25_1-neg50/50 H/D-Glycerol 0 negative
SA315387H-Glu/25_3-pos50/50 H/D-Glycerol 0 positive
SA315388H-Glu/25_2-pos50/50 H/D-Glycerol 0 positive
SA315389H-Glu/25_1-pos50/50 H/D-Glycerol 0 positive
SA315390H-Glu/75_1-neg50/50 H/D-Glycerol 100 negative
SA315391H-Glu/75_repeat_2-neg50/50 H/D-Glycerol 100 negative
SA315392H-Glu/75_repeat_1-neg50/50 H/D-Glycerol 100 negative
SA315393H-Glu/75_3-neg50/50 H/D-Glycerol 100 negative
SA315394H-Glu/75_2-neg50/50 H/D-Glycerol 100 negative
SA315395H-Glu/75_repeat_3-neg50/50 H/D-Glycerol 100 negative
SA315396H-Glu/75_3-pos50/50 H/D-Glycerol 100 positive
SA315397H-Glu/75_1-pos50/50 H/D-Glycerol 100 positive
SA315398H-Glu/75_2-pos50/50 H/D-Glycerol 100 positive
SA315399D-Glu/100-neg_tech-rep1D-Glucose 0 negative
SA315400D-Glu/100-neg_tech-rep2D-Glucose 0 negative
SA315401D-Glu/100-posD-Glucose 0 positive
SA31540250D-Gly/100_2-negD-Glucose 100 negative
SA31540350D-Gly/100_3-negD-Glucose 100 negative
SA31540450D-Gly/100_1-negD-Glucose 100 negative
SA31540550D-Gly/100_1-posD-Glucose 100 positive
SA31540650D-Gly/100_2-posD-Glucose 100 positive
SA31540750D-Gly/100_3-posD-Glucose 100 positive
SA315408H-Glu/50_1-negD-Glycerol 0 negative
SA315409H-Glu/50_2-negD-Glycerol 0 negative
SA315410H-Glu/50_3-negD-Glycerol 0 negative
SA315411H-Glu/50_2-posD-Glycerol 0 positive
SA315412H-Glu/50_3-posD-Glycerol 0 positive
SA315413H-Glu/50_1-posD-Glycerol 0 positive
SA315414H-Glu/100-neg_tech-rep2D-Glycerol 100 negative
SA315415H-Glu/100-neg_tech-rep1D-Glycerol 100 negative
SA315416H-Glu/100-posD-Glycerol 100 positive
SA31541750D-Gly/0_1-negH-Glucose 100 negative
SA31541850D-Gly/0_2-negH-Glucose 100 negative
SA31541950D-Gly/0_3-negH-Glucose 100 negative
SA31542050D-Gly/0_2-posH-Glucose 100 positive
SA31542150D-Gly/0_1-posH-Glucose 100 positive
SA31542250D-Gly/0_3-posH-Glucose 100 positive
SA315423D-Glu/0_3-negH-Glucose 25 negative
SA315424D-Glu/0_2-negH-Glucose 25 negative
SA315425D-Glu/0_1-negH-Glucose 25 negative
SA315426D-Glu/0_2-posH-Glucose 25 positive
SA315427D-Glu/0_1-posH-Glucose 25 positive
SA315428D-Glu/0_3-posH-Glucose 25 positive
SA315429D-Gly/0_2-negH-Glucose 50 negative
SA315430D-Gly/0_1-negH-Glucose 50 negative
SA315431D-Gly/0_3-negH-Glucose 50 negative
SA315432D-Gly/0_3-posH-Glucose 50 positive
SA315433D-Gly/0_2-posH-Glucose 50 positive
SA315434D-Gly/0_1-posH-Glucose 50 positive
SA315435D-Gly/100_2-negH-Glucose 75 negative
SA315436D-Gly/100_3-negH-Glucose 75 negative
SA315437D-Gly/100_1-negH-Glucose 75 negative
SA315438D-Gly/100_3-posH-Glucose 75 positive
SA315439D-Gly/100_1-posH-Glucose 75 positive
SA315440D-Gly/100_2-posH-Glucose 75 positive
SA315441H-Gly/0-neg_tech-rep2H-Glycerol 0 negative
SA315442H-Gly/0-neg_tech-rep1H-Glycerol 0 negative
SA315443H-Gly/0-posH-Glycerol 0 positive
SA315444H-Gly/100_1-negH-Glycerol 100 negative
SA315445H-Gly/100_2-negH-Glycerol 100 negative
SA315446H-Gly/100_3-negH-Glycerol 100 negative
SA315447H-Gly/100_3-posH-Glycerol 100 positive
SA315448H-Gly/100_2-posH-Glycerol 100 positive
SA315449H-Gly/100_1-posH-Glycerol 100 positive
SA315450H-Gly/25-neg_tech-rep2H-Glycerol 25 negative
SA315451H-Gly/25-neg_tech-rep1H-Glycerol 25 negative
SA315452H-Gly/25-posH-Glycerol 25 positive
SA315453H-Gly/50-neg_tech-rep1H-Glycerol 50 negative
SA315454H-Gly/50-neg_tech-rep2H-Glycerol 50 negative
SA315455H-Gly/50-posH-Glycerol 50 positive
SA315456H-Gly/75-neg_tech-rep2H-Glycerol 75 negative
SA315457H-Gly/75-neg_tech-rep1H-Glycerol 75 negative
SA315458H-Gly/75-posH-Glycerol 75 positive
Showing results 1 to 75 of 75

Collection:

Collection ID:CO002996
Collection Summary:Lipids were extracted from E coli cell pellets following the Matyash protocol with slight variations described in the manuscript supplemental. Cell lysis was performed with bead beating or ultrasonication. Extraction solvents were in the ratio 10:3:25 MTBE:methanol:water. See publication for more detail.
Collection Protocol Filename:Deuterated_Lipids_Methods_Summary.pdf
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR003012
Treatment Summary:E. coli was grown in Enfors minimal media (deuterated or otherwise) with different carbon sources including glycerol, glucose, D-glycerol, and D-glucose.
Cell Media:Enfors minimal media
Cell Harvesting:30 mL culture collected by centrifugation at 4k x g

Sample Preparation:

Sampleprep ID:SP003009
Sampleprep Summary:Lipids were extracted from E coli cell pellets following the Matyash protocol with slight variations described in the manuscript supplemental. Cell lysis was performed with bead beating or ultrasonication. Extraction solvents were in the ratio 10:3:25 MTBE:methanol:water. See publication for more detail.
Sampleprep Protocol Filename:Deuterated_Lipids_Methods_Summary.pdf
Extraction Method:Matyash (MTBE) varient
Sample Resuspension:8:23:69 butanol:isopropanol:water

Combined analysis:

Analysis ID AN004748 AN004749
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column In-house packed nano column (ID 100 μm, Kinetex 1.7 μm C18 (100 Å) [Phenomenex], 12-15 cm. In-house packed nano column (ID 100 μm, Kinetex 1.7 μm C18 (100 Å) [Phenomenex], 12-15 cm.
MS Type ESI ESI
MS instrument type LTQ-FT LTQ-FT
MS instrument name Thermo Velos Pro Orbitrap Thermo Velos Pro Orbitrap
Ion Mode NEGATIVE POSITIVE
Units Presence/Absence Presence/Absence

Chromatography:

Chromatography ID:CH003581
Chromatography Summary:Because the columns were packed in-house, there is some variation in the total length (see column description below).
Methods Filename:Deuterated_Lipids_Methods_Summary.pdf
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:In-house packed nano column (ID 100 μm, Kinetex 1.7 μm C18 (100 Å) [Phenomenex], 12-15 cm.
Column Temperature:room temp
Flow Gradient:Solvent Gradient: Time (min) 0 1 2.5 7.5 13.5 48.5 58.5 75.5 77.5 87 Solvent A (%) 99 99 70 65 45 30 1 1 99 99 Solvent B (%) 1 1 30 45 55 70 99 99 1 1
Flow Rate:Split flow nano-chromatography. The actual flow rate at the column is dependent on a variety of factors and an accurate measurement of the flow rate is impractical. The flow rate at the macro pumps were set at either 0.05 or 0.1 mL/min depending on the waste line's backpressure.
Solvent A:60% acetonitrile/40% water; ~0.4g/L ammonium acetate
Solvent B:90% sopropanol/10% acetonitrile; ~0.4g/L ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS004494
Analysis ID:AN004748
Instrument Name:Thermo Velos Pro Orbitrap
Instrument Type:LTQ-FT
MS Type:ESI
MS Comments:Top 10 DDA acquisition: Oribitrap Full-Scan at 30k resolving power from 150-2000 m/z. Data-dependent collisional-induced dissociation (CID) fragmentation scans performed with the LTQ ion trap at 30 normalized collision energy with normal scan rate.
Ion Mode:NEGATIVE
Analysis Protocol File:Deuterated_Lipids_Methods_Summary.pdf
  
MS ID:MS004495
Analysis ID:AN004749
Instrument Name:Thermo Velos Pro Orbitrap
Instrument Type:LTQ-FT
MS Type:ESI
MS Comments:Top 10 DDA acquisition: Oribitrap Full-Scan at 30k resolving power from 150-2000 m/z. Data-dependent collisional-induced dissociation (CID) fragmentation scans performed with the LTQ ion trap at 30 normalized collision energy with normal scan rate.
Ion Mode:POSITIVE
Analysis Protocol File:Deuterated_Lipids_Methods_Summary.pdf
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