Summary of Study ST002348

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 PR001508. The data can be accessed directly via it's Project DOI: 10.21228/M8RX35 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.

Study ID	ST002348
Study Title	Comparative metabolite profiling of glycolytic and sulfoglycolytic E. coli
Study Summary	Glycolytic E. coli (E. coli grown on glucose as a sole carbon source) and sulfoglycolytic E. coli (E. coli grown on the sulfosugar sulfoquinovose as a sole carbon source) were grown to mid-log phase in M9 minimal medium. Samples were harvested at mid-log phase and analysed using GC-EI-QqQ-MS.
Institute	University of Melbourne
Last Name	Williams
First Name	Spencer
Address	05, 532, David Penington Building, Parkville, 3010, VIC, Australia
Email	sjwill@unimelb.edu.au
Phone	+61383442422
Submit Date	2022-11-14
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	GC-MS
Release Date	2022-11-28
Release Version	1

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Project:

Project ID:	PR001508
Project DOI:	doi: 10.21228/M8RX35
Project Title:	Metabolite profiling of glycolytic and sulfoglycolytic E. coli
Project Summary:	Targeted comparative metabolite profiling of glucose-grown and sulfoquinovose-grown E. coli BW25113
Institute:	University of Melbourne
Last Name:	Williams
First Name:	Spencer
Address:	05, 532, David Penington Building, Parkville, 3010, VIC, Australia
Email:	sjwill@unimelb.edu.au
Phone:	+61383442422

Subject:

Subject ID:	SU002437
Subject Type:	Bacteria
Subject Species:	Escherichia coli
Taxonomy ID:	562
Genotype Strain:	BW25113

Factors:

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

mb_sample_id	local_sample_id	Factor
SA235658	JM Glc 1	Glc
SA235659	JM Glc 5	Glc
SA235660	JM Glc 6	Glc
SA235661	JM Glc 2	Glc
SA235662	JM Glc 4	Glc
SA235663	JM Glc 3	Glc
SA235664	PBQC 2	PBQC
SA235665	PBQC 3	PBQC
SA235666	PBQC 4	PBQC
SA235667	PBQC 1	PBQC
SA235668	JM SQ 3	SQ
SA235669	JM SQ 1	SQ
SA235670	JM SQ 2	SQ
SA235671	JM SQ 4	SQ
SA235672	JM SQ 5	SQ
SA235673	JM SQ 6	SQ

Showing results 1 to 16 of 16

Showing results 1 to 16 of 16

Collection:

Collection ID:	CO002430
Collection Summary:	Cells were metabolically arrested by infusing with ice-cold PBS and washed with PBS.
Sample Type:	Bacterial cells

Treatment:

Treatment ID:	TR002449
Treatment Summary:	E. coli adapted to growth on the relevant substrate was grown on M9 minimal medium containing either Glc or SQ as a sole carbon source until mid-log phase was achieved.

Sample Preparation:

Sampleprep ID:	SP002443
Sampleprep Summary:	Cell pellets were resuspended in chilled extraction solution (500 µL) comprised of 3:1 MeOH: H2O and (13C5, 15N)valine (1 mM, 0.5 µL) and (13C6)sorbitol (1 mM, 0.5 µL) as internal standards. The suspensions were subjected to freeze-thaw cycles to facilitate lysis of the cells (30 s in liquid N2, 30 s in a dry ice/EtOH bath for 10 cycles), and shaken (9000 rpm, 10 min, 2°C). The samples were then centrifuged (12700 rpm, 5 min, 1°C). The cell lysate supernatant was transferred into glass inserts and dried. All samples were washed with MeOH (50 µL). All samples were methoximated with methoxylamine hydrochloride solution (30 mg/mL in pyridine, 20 µL) for 2 h at 37°C, followed by trimethylsilyation in BSTFA + 1% TMCS (20 µL) for 1 h at 37°C with continuous mixing. Samples were incubated at rt for 1 h prior to GC-MS analysis.

Sampleprep ID:

SP002443

Sampleprep Summary:

Cell pellets were resuspended in chilled extraction solution (500 µL) comprised of 3:1 MeOH: H2O and (13C5, 15N)valine (1 mM, 0.5 µL) and (13C6)sorbitol (1 mM, 0.5 µL) as internal standards. The suspensions were subjected to freeze-thaw cycles to facilitate lysis of the cells (30 s in liquid N2, 30 s in a dry ice/EtOH bath for 10 cycles), and shaken (9000 rpm, 10 min, 2°C). The samples were then centrifuged (12700 rpm, 5 min, 1°C). The cell lysate supernatant was transferred into glass inserts and dried. All samples were washed with MeOH (50 µL). All samples were methoximated with methoxylamine hydrochloride solution (30 mg/mL in pyridine, 20 µL) for 2 h at 37°C, followed by trimethylsilyation in BSTFA + 1% TMCS (20 µL) for 1 h at 37°C with continuous mixing. Samples were incubated at rt for 1 h prior to GC-MS analysis.

Combined analysis:

Analysis ID	AN003833
Analysis type	MS
Chromatography type	GC
Chromatography system	Shimadzu GC-2010
Column	J&W DB-5 (30 m × 0.25mm,1.00um)
MS Type	EI
MS instrument type	Triple quadrupole
MS instrument name	Shimazu TQ8040
Ion Mode	UNSPECIFIED
Units	a.u.

Chromatography:

Chromatography ID:	CH002838
Instrument Name:	Shimadzu GC-2010
Column Name:	J&W DB-5 (30 m × 0.25mm,1.00um)
Chromatography Type:	GC

MS:

MS ID:	MS003575
Analysis ID:	AN003833
Instrument Name:	Shimazu TQ8040
Instrument Type:	Triple quadrupole
MS Type:	EI
MS Comments:	Please see attached file.
Ion Mode:	UNSPECIFIED