Summary of Study ST000466

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 PR000358. The data can be accessed directly via it's Project DOI: 10.21228/M8S302 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000466
Study TitleStreptococcus mutans organic acids/amino acid profiles, effect of oxidative stress; pilot
Study TypeAmino acid/organic acid profiles of wild-type and mutant strain in response to H2O2 treatment over time.
Study SummaryS. mutans UA159 and ΔspxA1 will be grown in BHI to OD600 = 0.4. Each culture will be split in to 4 samples. For the first sample, 3E10 cells will immediately be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. The remaining three samples will be treated with H2O2 to 0.5 mM, and the harvesting process repeated after 15, 30 and 60 minutes.
Institute
University of Florida
DepartmentSECIM
LaboratoryLemos-Abranches
Last NameHardin
First NameEmily
Address1395 Center Drive, PO Box 100424, Gainesville, FL 32610
Emailehardin@ufl.edu
Phone352-273-8844
Submit Date2016-09-08
Num Groups6
Total Subjects6
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2017-10-03
Release Version1
Emily Hardin Emily Hardin
https://dx.doi.org/10.21228/M8S302
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000358
Project DOI:doi: 10.21228/M8S302
Project Title:Streptococcus mutans Amino Acid/Organic Acid Profile
Project Summary:Determination of metabolite profiles of S. mutans strains UA159 (WT) and ΔspxA1 in response to oxidative stress
Institute:University of Florida
Department:Oral Biology
Laboratory:Lemos-Abranches
Last Name:Lemos
First Name:Jose
Address:1395 Center Drive, PO Box 100424 Gainesville, FL 32610
Email:jlemos@dental.ufl.edu
Phone:352-273-8843
Funding Source:UF start-up funds

Subject:

Subject ID:SU000487
Subject Type:Bacterial cells
Subject Species:Streptococcus mutans
Taxonomy ID:1309
Genotype Strain:UA159
Species Group:Bacteria

Factors:

Subject type: Bacterial cells; Subject species: Streptococcus mutans (Factor headings shown in green)

mb_sample_id local_sample_id Strain Exposure to H2O2
SA023598Lemos_010WT 0.00
SA023599Lemos_011WT 15 min
SA023600Lemos_012WT 30 min
SA023601Lemos_013WT 60 min
SA023602Lemos_014ΔspxA1 0.00
SA023603Lemos_017ΔspxA1 60 min
Showing results 1 to 6 of 6

Collection:

Collection ID:CO000481
Collection Summary:Upon reaching OD600 = 0.4, the culture is split into 4 samples. Three are treated with H2O2 (0.5 mM). The other is harvested by filtration onto 0.45uM nitrocellulose membrane. The cells will be scraped off of the membrane into ice-cold PBS (~1 mL), centrifuged for 30 seconds at 12K RPM, liquid aspirated and stored at -80C until sending for analysis. This process will be repeated with the remaining three samples after 15, 30 and 60 minutes treatment with H2O2.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR000501
Treatment Summary:0.5 mM H2O2 for 15, 30 and 60 minutes. Control has 0 H2O2 added.

Sample Preparation:

Sampleprep ID:SP000494
Sampleprep Summary:Amino acids|Organic acids
Sampleprep Protocol Filename:SB_AA_Assay.pdf
SB_OA_Assay.pdf

Combined analysis:

Analysis ID AN000728 AN000729
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 6490 Thermo Dionex Ultimate 3000
Column Waters AccQ Tag (100 x 2mm,1.7um) Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name Agilent 6490 QQQ Thermo Quantiva QQQ
Ion Mode POSITIVE POSITIVE
Units nmol/mg protein nmol/mg protein

Chromatography:

Chromatography ID:CH000521
Chromatography Summary:Amino acids
Methods Filename:SB_AA_Assay.pdf
Instrument Name:Agilent 6490
Column Name:Waters AccQ Tag (100 x 2mm,1.7um)
Column Temperature:55
Flow Rate:0.7 mL/min
Solvent A:AccQ·Tag Eluent A
Solvent B:accQ·Tag Eluent B
Chromatography Type:Reversed phase
  
Chromatography ID:CH000522
Chromatography Summary:Organic acids
Methods Filename:SB_OA_Assay.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:45
Flow Rate:0.3 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS000645
Analysis ID:AN000728
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000646
Analysis ID:AN000729
Instrument Name:Thermo Quantiva QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
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