Summary of Study ST000399

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 PR000312. The data can be accessed directly via it's Project DOI: 10.21228/M8KP4K This work is supported by NIH grant, U2C- DK119886.

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Study IDST000399
Study TitleE.coli effects on growth and substrate uptake of green algae (part I - HILIC)
Study SummaryThe purpose of this project was to quantify the exchange of thiamine between bacteria and algae. We previously observed that the model bacteria, Escherichia coli, enhanced the growth and substrate uptake of the green algae, Auxenochlorella protothecoides. We hypothesized that this growth enhancement was due to the secretion of thiamine derivatives or degradation products by E. coli followed by uptake of these compounds by A. protothecoides. Targeted and untargeted LCMS revealed the presence of thiamine dervatives in E. coli cell extracts. These LCMS methods were also used to quantify thiamine derivatives and two degradation products, HMP and THZ, present in E. coli medium after cell removal. The LCMS results along with culture studies were employed to show that thiamine derivatives and degradation products were the primary mechanism of symbiosis between E. coli and A. protothecoides.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2015-04-20
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-06-18
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8KP4K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Combined analysis:

Analysis ID AN000636 AN000637
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 6530 Agilent 6550
Column Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units counts counts

Chromatography:

Chromatography ID:CH000461
Methods Filename:Data_Dictionary_Fiehn_laboratory_HILIC_QTOF_MS.pdf
Instrument Name:Agilent 6530
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Pressure:200-700 bar
Column Temperature:45 C
Flow Gradient:100% B to 30% B
Flow Rate:0.4 mL/min
Injection Temperature:4 C
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:3uL
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3
Solvent B:100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3
Analytical Time:14 min
Capillary Voltage:4500 V
Time Program:16.75 min
Weak Wash Solvent Name:1:1 ACN:H2O
Strong Wash Solvent Name:1:1 ACN:H2O
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel generated
Chromatography Type:HILIC
  
Chromatography ID:CH000462
Methods Filename:Data_Dictionary_Fiehn_laboratory_HILIC_QTOF_MS.pdf
Instrument Name:Agilent 6550
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Pressure:200-700 bar
Column Temperature:45 C
Flow Gradient:100% B to 30% B
Flow Rate:0.4 mL/min
Injection Temperature:4 C
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:3uL
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3
Solvent B:95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate, pH 3
Analytical Time:14 min
Capillary Voltage:4500 V
Time Program:16.75 min
Weak Wash Solvent Name:1:1 ACN:H2O
Strong Wash Solvent Name:1:1 ACN:H2O
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel generated
Chromatography Type:HILIC
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