Summary of Study ST000119

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 PR000106. The data can be accessed directly via it's Project DOI: 10.21228/M8RC75 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000119
Study TitleMetabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family LCMS
Study Typewildtype vs knock-out
Study SummaryMetabolomics analysis of wild-type S. enterica, single RidA knock-out and triple Rid (ridA Rid2 Rid7) knock-out S.enterica cells
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryFiehn Laboratory
Last NameElBadawi-Sidhu
First NameMona
Address451 Health Sciences Drive, Davis, California 95616, USA
Emailmmelbadawi@ucdavis.edu
Submit Date2014-11-06
Num Groups4
Total Subjects6
Study CommentsSamples were measured in poitive and negative ionization mode. MS/MS files contain product ion scans (MS/MS) spectra for compound identification.
Raw Data AvailableNo
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2014-11-06
Release Version1
Mona ElBadawi-Sidhu Mona ElBadawi-Sidhu
https://dx.doi.org/10.21228/M8RC75
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000106
Project DOI:doi: 10.21228/M8RC75
Project Title:Metabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family
Institute:University of California, Davis
Department:Genome Center
Laboratory:Fiehn Laboratory
Last Name:Fiehn
First Name:Oliver
Address:451 Health Sciences Drive, Davis, California 95616, USA
Email:ofiehn@ucdavis.edu
Funding Source:U.S. National Science Foundation award MCB-1153413

Subject:

Subject ID:SU000138
Subject Type:Bacterial cells
Subject Species:Salmonella enterica;Escherichia coli
Taxonomy ID:28901;562
Genotype Strain:DM14100|Salmonella enterica subsp. enterica serovar Typhimurium str. LT2|K 12 MG1655|K 12 MG1655 ridA3::tn10 ΔyoaB624::cat STM1549-26::kan| | |yjeF::kan
Species Group:Bacteria

Factors:

Subject type: Bacterial cells; Subject species: Salmonella enterica;Escherichia coli (Factor headings shown in green)

mb_sample_id local_sample_id Strain Genotype
SA006213041113_EcoliCells_WT_R1_0005E.coli Wild-type
SA006214041113_EcoliCells_WT_R2_0060E.coli Wild-type
SA006215041113_EcoliCells_WT_Pool_MSMS_0064E.coli Wild-type
SA006216041113_EcoliCells_WT_R3_0044E.coli Wild-type
SA006217041113_EcoliCells_WT_R4_0034E.coli Wild-type
SA006218041113_EcoliCells_WT_R6_0023E.coli Wild-type
SA006219041113_EcoliCells_WT_R5_0037E.coli Wild-type
SA006206041113_EcoliCells_Yjef_R4_0038E.coli Δyjef Knock-out
SA006207041113_EcoliCells_Yjef_R5_0042E.coli Δyjef Knock-out
SA006208041113_EcoliCells_Yjef_R6_0025E.coli Δyjef Knock-out
SA006209041113_EcoliCells_Yjef_R2_0059E.coli Δyjef Knock-out
SA006210041113_EcoliCells_Yjef_Pool_MSMS_0066E.coli Δyjef Knock-out
SA006211041113_EcoliCells_Yjef_R3_0011E.coli Δyjef Knock-out
SA006212041113_EcoliCells_Yjef_R1_0049E.coli Δyjef Knock-out
SA006220041213_SentericaCells_RidAKO_R6_0055S.enterica RidA Knock-out
SA006221041113_SentericaCells_RidAKO_Pool_MSMS_0070S.enterica RidA Knock-out
SA006222041213_SentericaCells_RidAKO_R3_0029S.enterica RidA Knock-out
SA006223041213_SentericaCells_RidAKO_R4_0057S.enterica RidA Knock-out
SA006224041213_SentericaCells_RidAKO_R5_0035S.enterica RidA Knock-out
SA006225041213_SentericaCells_RidAKO_R2_0047S.enterica RidA Knock-out
SA006226041213_SentericaCells_RidAKO_R1_0022S.enterica RidA Knock-out
SA006227041113_SentericaCells_WT_Pool_MSMS_0068S.enterica Wild-type
SA006228041213_SentericaCells_WT_R6_0050S.enterica Wild-type
SA006229041213_SentericaCells_WT_R2_0058S.enterica Wild-type
SA006230041213_SentericaCells_WT_R3_0043S.enterica Wild-type
SA006231041213_SentericaCells_WT_R4_0021S.enterica Wild-type
SA006232041213_SentericaCells_WT_R5_0019S.enterica Wild-type
SA006233041213_SentericaCells_WT_R1_0048S.enterica Wild-type
Showing results 1 to 28 of 28

Collection:

Collection ID:CO000122
Collection Summary:-
Sample Type:Bacterial Cells
Collection Method:6 independent colonies of each cell line were grown in M9 minimal medium at 37C until OD600 reached 1.5-2.0. An equivalent of 1 mL at OD 2.0 was placed into a 1.5 mL Eppi tube and spun for 15 sec. After removal of a 0.5 mL medium aliquot, remaining medium was removed and cell pellet was frozen in liquid nitrogen.
Collection Location:University of Florida, Gainesville
Collection Vials:1.5 mL eppendorf tube
Storage Vials:1.5 mL eppendorf tube

Treatment:

Treatment ID:TR000140

Sample Preparation:

Sampleprep ID:SP000135
Sampleprep Summary:-
Processing Storage Conditions:on ice
Extraction Method:1.1 mL of cold, degassed extraction solvent (3:1 Methanol:Water) was added to each sample. Samples were vortexed for 20 sec then placed in sonicator for 5 min, followed by another 20 sec vortex. Samples were placed in -20C for 30 minutes prior to spinning down in centrifuge at 14 rcf for 5 min. The supernatant was transferred to 1.5 mL eppendorf tubes and evaporated in the Labconco speed vac.
Extract Storage:-80C
Sample Resuspension:H20 + 5mM NH4OAc + 0.2% Acetic Acid

Combined analysis:

Analysis ID AN000200 AN000201
Chromatography ID CH000133 CH000133
MS ID MS000163 MS000164
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1290 Agilent 1290
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 6530 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH000133
Chromatography Summary:Untargeted LC MS
Instrument Name:Agilent 1290
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Pressure:300 bar (max)
Column Temperature:40 C
Flow Gradient:0 - 4 min: 0% B; 4-12 min: linear gradient to 45% B; 12-20 min: 45% B
Flow Rate:0.25 mL/min
Injection Temperature:4C
Sample Injection:5 uL
Solvent A:100% water; 0.2% acetic acid; 5mM ammonium acetate
Solvent B:90% acetonitrile/10% water; 0.2% acetic acid; 5 mM ammonium acetate
Oven Temperature:H20 + 5mM NH4OAc + 0.2% Acetic Acid
Time Program:20 min
Weak Wash Solvent Name:50:50 Methanol:Water
Weak Wash Volume:15 seconds
Target Sample Temperature:Autosampler temperature 4C
Randomization Order:Excel generated
Chromatography Type:HILIC

MS:

MS ID:MS000163
Analysis ID:AN000200
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3000
Collision Energy:Ramped 0.02eV/m/z + 10 eV
Collision Gas:Nitrogen
Dry Gas Flow:Nebulizer: 10 L/min Sheath: 9 L/min
Dry Gas Temp:Nebulizer and Sheath: 350
Fragment Voltage:125
Ionization:Positive
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Dataformat:.d
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:100 - 1700 m/z
Scanning Cycle:2
  
MS ID:MS000164
Analysis ID:AN000201
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:3000
Collision Energy:Ramped 0.02eV/m/z + 10 eV
Collision Gas:Nitrogen
Dry Gas Flow:Nebulizer: 10 L/min Sheath: 9 L/min
Dry Gas Temp:Nebulizer and Sheath: 350
Fragment Voltage:125
Ionization:Negative
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Dataformat:.d
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:100 - 1700 m/z
Scanning Cycle:2
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