Summary of Study ST002287

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001467. The data can be accessed directly via it's Project DOI: 10.21228/M83H68 This work is supported by NIH grant, U2C- DK119886.


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 IDST002287
Study TitleEnhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile
Study SummaryLC-MS data from the supernatant and cell pellet of cultured commensal E. coli with and without mutations in outer membrane porin C
University of Calgary
DepartmentMicrobiology and Infectious Disease
Last NameBrown
First NameKirsty
AddressHSC 1729, 3330 Hospital Dr NW
Submit Date2022-09-26
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-05-04
Release Version1
Kirsty Brown Kirsty Brown application/zip

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Project ID:PR001467
Project DOI:doi: 10.21228/M83H68
Project Title:Enhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile
Project Summary:LC-MS profiles of supernatant and cell pellet of bacterial culture from commensal E. coli strains with different immunogenicity.
Institute:University of Calgary
Department:Microbiology and Infectious Disease
Last Name:Brown
First Name:Kirsty
Address:HSC 1729, 3330 Hospital Dr NW
Phone:250 869 2232
Funding Source:Canadian Institute of Health Research
Publications:Enhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile
Contributors:Regula Burkhard1, Mia Koegler1, Kirsty Brown2, Kirsten Wilson1, Lukas Mager2, Amanda Zucoloto2, Carolyn Thomson2, Roopa Hebbandi Nanjundappa1, Braedon McDonald1,3,4, Kathy D. McCoy2,3,4, and Markus B. Geuking1,3,4,*


Subject ID:SU002373
Subject Type:Bacteria
Subject Species:Escherichia coli
Taxonomy ID:562


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

mb_sample_id local_sample_id sample_site strain biologial_rep technical_rep
SA219142Intra_GP61_1_1Intra GP61 1 1
SA219143Intra_GP61_1_2Intra GP61 1 2
SA219144Intra_GP61_4_1Intra GP61 4 1
SA219145Intra_GP61_4_2Intra GP61 4 2
SA219146Intra_GP61_4_3Intra GP61 4 3
SA219147Intra_GP61_4_4Intra GP61 4 4
SA219148Intra_KO_1_1Intra KO 1 1
SA219149Intra_KO_1_2Intra KO 1 2
SA219150Intra_KO_4_1Intra KO 4 1
SA219151Intra_KO_4_2Intra KO 4 2
SA219152Intra_KO_4_3Intra KO 4 3
SA219153Intra_KO_4_4Intra KO 4 4
SA219154Intra_WT_1_1Intra WT 1 1
SA219155Intra_WT_1_2Intra WT 1 2
SA219156Intra_WT_4_1Intra WT 4 1
SA219157Intra_WT_4_2Intra WT 4 2
SA219158Intra_WT_4_3Intra WT 4 3
SA219159Intra_WT_4_4Intra WT 4 4
SA219160SN_GP61_1_1SN GP61 1 1
SA219161SN_GP61_1_2SN GP61 1 2
SA219162SN_GP61_4_1SN GP61 4 1
SA219163SN_GP61_4_2SN GP61 4 2
SA219164SN_GP61_4_3SN GP61 4 3
SA219165SN_GP61_4_4SN GP61 4 4
SA219166SN_KO_1_1SN KO 1 1
SA219167SN_KO_1_2SN KO 1 2
SA219168SN_KO_4_1SN KO 4 1
SA219169SN_KO_4_2SN KO 4 2
SA219170SN_KO_4_3SN KO 4 3
SA219171SN_KO_4_4SN KO 4 4
SA219172SN_WT_1_1SN WT 1 1
SA219173SN_WT_1_2SN WT 1 2
SA219174SN_WT_4_1SN WT 4 1
SA219175SN_WT_4_2SN WT 4 2
SA219176SN_WT_4_3SN WT 4 3
SA219177SN_WT_4_4SN WT 4 4
Showing results 1 to 36 of 36


Collection ID:CO002366
Collection Summary:The different E. coli strains were grown in LB media and subcultured to OD600 = 0.5.
Sample Type:Bacterial cells


Treatment ID:TR002385
Treatment Summary:E.coli strains were either wild type (MG1655), were deficient in outer membrane porin (OmpC KO) or had a viral epitope from LCMV in place of the OmpC (GP61)

Sample Preparation:

Sampleprep ID:SP002379
Sampleprep Summary:Metabolites from supernatant were extracted in 100% methanol, precipitated at -20°C for 1 hour, centrifuged and diluted into a linear range (1:20 final dilution) with 50% methanol. To extract intracellular metabolites, bacterial pellet was snap-frozen in liquid nitrogen, resuspended in cell lysis buffer (1M Tris, 5M NaCL, 0.5M EDTA, 10% SDS in H2O) and sonicated. Metabolites were extracted as described above

Combined analysis:

Analysis ID AN003739
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Vanquish
Column Thermo Syncronis HILIC (100 x 2.1mm,1.7um)
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Units AUC


Chromatography ID:CH002770
Methods Filename:protocol.docx
Instrument Name:Thermo Vanquish
Column Name:Thermo Syncronis HILIC (100 x 2.1mm,1.7um)
Column Temperature:30C
Flow Gradient:2 stage linear gradient
Flow Rate:600uL/min
Solvent A:100% water; 20 mM ammonium formate, pH 3
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:HILIC


MS ID:MS003487
Analysis ID:AN003739
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Comments:50-750 m/z, peak integration and assignment using El-Maven software matching to authentic standard library (~150 compounds).