Summary of Study ST001664

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 PR001069. The data can be accessed directly via it's Project DOI: 10.21228/M8HQ3X 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 IDST001664
Study TitleE.coli K-12 treated by IPL - analysis of polar phase (part-II)
Study SummaryE.coli K-12 cells were treated by IPL, extracted and separated into organic/lipid phase and polar phase. Chemical derivatization with dansyl chloride was applied for analysis of amino acids in the polar phase extraction.
Institute
University of Minnesota
Last NameChen
First NameChi
Address1334 Eckles Ave, St Paul, Minnesota, 55108, USA
Emailchichen@umn.edu
Phone6126247704
Submit Date2021-01-25
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2021-02-17
Release Version1
Chi Chen Chi Chen
https://dx.doi.org/10.21228/M8HQ3X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001069
Project DOI:doi: 10.21228/M8HQ3X
Project Title:Effect of IPL on E.coli Metabolome hydrophilic phase
Project Type:Untargeted LC-MS metabolomic study
Project Summary:Intense pulsed light (IPL) is becoming a new technical platform for disinfecting food against pathogenic bacteria. Metabolic changes are deemed to occur in bacteria as either the causes or the consequences of IPL-elicited bactericidal and bacteriostatic effects. However, little is known about the influences of IPL on bacterial metabolome. In this study, the IPL treatment was applied to E. coli K-12 for 0-20s, leading to time- and dose-dependent reductions in colony-forming units (CFU) and morphological changes. Cytoplasmic metabolites of the control and IPL-treated E. coli were examined by the liquid chromatography-mass spectrom-etry (LC-MS)-based metabolomic fingerprinting. The results from multivariate modeling and marker identification indicated that the metabolites in redox response, glycolysis, amino acid and nucleotide metabolism were selectively affected by the IPL treatments.
Institute:University of Minnesota
Last Name:Chen
First Name:Chi
Address:1334 Eckles Ave, St Paul, Minnesota, 55108, USA
Email:chichen@umn.edu
Phone:6126247704

Subject:

Subject ID:SU001741
Subject Type:Bacteria
Subject Species:Escherichia coli
Taxonomy ID:562
Subject Comments:E. coli strain K-12 W3110

Factors:

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

mb_sample_id local_sample_id Treatment
SA152210ctl_2control
SA152211ctl_1control
SA152212ctl_3control
SA152213ctl_4control
SA15219410s_2IPL 10 s
SA15219510s_4IPL 10 s
SA15219610s_1IPL 10 s
SA15219710s_3IPL 10 s
SA15219815s_3IPL 15 s
SA15219915s_4IPL 15 s
SA15220015s_2IPL 15 s
SA15220115s_1IPL 15 s
SA15220220s_1IPL 20 s
SA15220320s_2IPL 20 s
SA15220420s_3IPL 20 s
SA15220520s_4IPL 20 s
SA1522065s_3IPL 5 s
SA1522075s_4IPL 5 s
SA1522085s_1IPL 5 s
SA1522095s_2IPL 5 s
Showing results 1 to 20 of 20

Collection:

Collection ID:CO001734
Collection Summary:E.coli strain K-12 was cultured in LB broth and harvested at OD=1. After centrifuge, cell pellets were harvested and washed with PBS twice. Then the pellet was re-suspended in PBS for further treatment.
Collection Protocol Filename:Cell_culture_IPL_treatment_Sample_preparation_method.docx
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001754
Treatment Summary:For each IPL treatment, a 30 mL K-12 suspension in PBS was loaded in a petri dish (15 cm diameter) and then placed under the broad-spectrum light (wavelength 190-1100 nm) in a Z-1000 SteriPulse-XL system (Xenon Corporation, Woburn, MA). The samples were treated with the IPL for 0, 5, 10, 15, and 20 s.
Treatment Protocol Filename:Cell_culture_IPL_treatment_Sample_preparation_method.docx

Sample Preparation:

Sampleprep ID:SP001747
Sampleprep Summary:The control and IPL-treated E. coli samples were centrifuged for obtaining the pellets, which were then washed with PBS twice. After extraction with methanol-water-chloroform, the polar phase was separated and derivatized with dansyl chloride (DC) for amino acid analysis.
Sampleprep Protocol Filename:Cell_culture_IPL treatment_Sample preparation_method.docx

Combined analysis:

Analysis ID AN002716
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity
Column Waters Acquity BEH C18 (50 x 2.1mm,1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name Waters Xevo-G2-S
Ion Mode POSITIVE
Units no applicable unites

Chromatography:

Chromatography ID:CH002004
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (50 x 2.1mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002513
Analysis ID:AN002716
Instrument Name:Waters Xevo-G2-S
Instrument Type:QTOF
MS Type:ESI
MS Comments:Features were captured by MarkerLynx (Waters) and processed. The relative intensity of each ion was calculated by normalizing the single ion counts (SIC) versus the total ion counts (TIC) in the whole chromatogram, while setting the TIC arbitrarily to 10,000.
Ion Mode:POSITIVE
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