Summary of Study ST001264

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 PR000849. The data can be accessed directly via it's Project DOI: 10.21228/M8Z090 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 ID	ST001264
Study Title	Antibiotics and Dietary Minerals Lipidomics
Study Summary	Plasma samples from Wistar rats fed a control or High-sodium and low-potassium HNaLK diet with or without antibiotic treatment (n = 7 each, a total of 28) were subjected to lipidomics analysis.The HNaLK diet interacts with gut bacteria to alter plasma lipid profiles, which may be related to its health effects.
Institute	University of California, Davis
Last Name	Folz
First Name	Jacob
Address	451 Health Sciences Dr., Davis, CA, 95616
Email	jfolz@ucdavis.edu
Phone	7155636311
Submit Date	2019-10-06
Num Groups	4
Total Subjects	28
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2020-01-06
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000849
Project DOI:	doi: 10.21228/M8Z090
Project Title:	Antibiotics and Dietary Minerals Lipidomics
Project Type:	Untargeted Mass Spectrometry
Project Summary:	Rats were fed either high sodium/ low potassium diet or low sodium/ high potassium diet, and either antibiotics, or no antibiotics. Plasma samples were analyzed using UHPLC MS/MS methodology.
Institute:	University of California, Davis
Laboratory:	Oliver Fiehn
Last Name:	Folz
First Name:	Jacob
Address:	451 Health Science Drive, Davis, CA 95616
Email:	jfolz@ucdavis.edu
Phone:	7155636311
Contributors:	Jacob Folz, Young Taek Oh, Ivana Blaženović, Joyce Richey, Oliver Fiehn and Jang H. Youn

Subject:

Subject ID:	SU001332
Subject Type:	Mammal
Subject Species:	Rattus norvegicus
Taxonomy ID:	10116
Age Or Age Range:	10 weeks
Gender:	Male
Animal Animal Supplier:	Envigo Laboratories
Animal Light Cycle:	12-h light, 6 AM–6 PM; 12-h dark, 6 PM–6 AM

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA091972	Sample23	Antibiotics_High Potasium / Low Sodium
SA091973	Sample27	Antibiotics_High Potasium / Low Sodium
SA091974	Sample13	Antibiotics_High Potasium / Low Sodium
SA091975	Sample18	Antibiotics_High Potasium / Low Sodium
SA091976	Sample12	Antibiotics_High Potasium / Low Sodium
SA091977	Sample8	Antibiotics_High Potasium / Low Sodium
SA091978	Sample1	Antibiotics_High Potasium / Low Sodium
SA091979	Sample17	Antibiotics_Low Potasium / High Sodium
SA091980	Sample28	Antibiotics_Low Potasium / High Sodium
SA091981	Sample14	Antibiotics_Low Potasium / High Sodium
SA091982	Sample11	Antibiotics_Low Potasium / High Sodium
SA091983	Sample2	Antibiotics_Low Potasium / High Sodium
SA091984	Sample24	Antibiotics_Low Potasium / High Sodium
SA091985	Sample7	Antibiotics_Low Potasium / High Sodium
SA091989	Sample21	None (normal)_High Potasium / Low Sodium
SA091990	Sample20	None (normal)_High Potasium / Low Sodium
SA091991	Sample25	None (normal)_High Potasium / Low Sodium
SA091992	Sample10	None (normal)_High Potasium / Low Sodium
SA091993	Sample3	None (normal)_High Potasium / Low Sodium
SA091994	Sample15	None (normal)_High Potasium / Low Sodium
SA091995	Sample6	None (normal)_High Potasium / Low Sodium
SA091996	Sample22	None (normal)_Low Potasium / High Sodium
SA091997	Sample26	None (normal)_Low Potasium / High Sodium
SA091998	Sample19	None (normal)_Low Potasium / High Sodium
SA091999	Sample9	None (normal)_Low Potasium / High Sodium
SA092000	Sample4	None (normal)_Low Potasium / High Sodium
SA092001	Sample5	None (normal)_Low Potasium / High Sodium
SA092002	Sample16	None (normal)_Low Potasium / High Sodium
SA091986	Biorec2	No Treatment
SA091987	Biorec3	No Treatment
SA091988	Biorec1	No Treatment

Showing results 1 to 31 of 31

Showing results 1 to 31 of 31

Collection:

Collection ID:	CO001326
Collection Summary:	After the one-week feeding, animals were anesthetized with isoflurane at ~7 AM, and blood samples for lipidomics analysis were collected using a heparinized syringe through the abdominal aorta. Blood samples were rapidly spun, and plasma was isolated and frozen immediately in liquid N2. The plasma samples were stored at -80°C until analysis.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR001347
Treatment Summary:	Animals were fed for 1 week with diets containing different amounts of Na+ and K+ (n = 7 for each diet; a total of 14 rats). The diets were prepared from K+-deficient powdered rat diet (TD.88239.PWD; Envigo Teklad) with or without supplementation with KCl or NaCl.[10] The control (healthy) diet contained 0.29% Na+, which is the level in normal rat diets, and 2% K+, which is higher than the normal 1%. In the HNaLK diet, Na+ content was increased from 0.29% to 0.79%, a level similar to those in Western diets,[14] and K+ content was decreased to 0.1%, which was selected to be low, but not low enough to deplete plasma K+. The diets were gelled by heating, dissolving 30 g agarose in 500 mL of deionized water, and adding to 500 g of powdered diet supplemented with KCl and NaCl.

Treatment ID:

TR001347

Treatment Summary:

Animals were fed for 1 week with diets containing different amounts of Na+ and K+ (n = 7 for each diet; a total of 14 rats). The diets were prepared from K+-deficient powdered rat diet (TD.88239.PWD; Envigo Teklad) with or without supplementation with KCl or NaCl.[10] The control (healthy) diet contained 0.29% Na+, which is the level in normal rat diets, and 2% K+, which is higher than the normal 1%. In the HNaLK diet, Na+ content was increased from 0.29% to 0.79%, a level similar to those in Western diets,[14] and K+ content was decreased to 0.1%, which was selected to be low, but not low enough to deplete plasma K+. The diets were gelled by heating, dissolving 30 g agarose in 500 mL of deionized water, and adding to 500 g of powdered diet supplemented with KCl and NaCl.

Sample Preparation:

Sampleprep ID:	SP001340
Sampleprep Summary:	Samples (40uL plasma) were extracted using biphasic extraction technique adapted from Matyash et al. 2008. In summary 225 µL LC-MS grade methanol was added to plasma in 2 mL Eppendorf tube, vortexed for 10 seconds, followed by addition of 750 µL methyl tert-butyl ether (MTBE). Each sample was then vortexed for 10 seconds, shook on orbital shaker at maximum speed for six minutes, followed by addition of 188 µL LC-MS grade water. Finally, each sample was vortexed for 10 seconds and centrifuged for 2 minutes at 14,000 rpm. The top phase of the biphasic solution was aliquoted into 1.5 mL microcentrifuge tubes for 350 µL aliquots of MTBE phase. Extraction was carried out at 4°C. All extract tubes were dried under vacuum and frozen at -80°C until LC-MS/MS analysis. Lipidomics analysis followed methods of Cajka et al. 2017 (doi: 10.1021/acs.analchem.7b03404). Non-polar lipids were analyzed on Vanquish Focused UHPLC coupled to a Q-Exactive HF mass spectrometer (ThermoFisher Scientific). Liquid chromatography used a Waters Acquity UPLC CSH C18 column (100mm x 2.1mm, 1.7 μm particle size) coupled to an Acquity UPLC CSH C18 VanGuard precolumn (5 x 2.1 mm; 1.7 μm) (Waters, Milford, MA) with mobile phases of 60:40 (v/v) acetonitrile/ water, and 90:10 (v/v) isopropanol/acetonitrile, both of which had 10 mM ammonium formate and 0.1% formic acid for positive mode ionization analysis, and 10 mM ammonium acetate and 0.1% acetic acid for negative mode ionization analysis. Three and five microliters of reconstituted sample were injected onto column for positive and negative mode ionization analysis respectively. Mobile phase gradient was identical to that of Cajka et al. Data were collected in data dependent manner with the top four ions from each MS1 scan being selected for MS/MS fragmentation. A scan range from 120 to 1200 m/z was used for this analysis. Samples were analyzed in a randomized order with a method blank and quality control plasma sample analyzed between every ten samples.

Sampleprep ID:

SP001340

Sampleprep Summary:

Samples (40uL plasma) were extracted using biphasic extraction technique adapted from Matyash et al. 2008. In summary 225 µL LC-MS grade methanol was added to plasma in 2 mL Eppendorf tube, vortexed for 10 seconds, followed by addition of 750 µL methyl tert-butyl ether (MTBE). Each sample was then vortexed for 10 seconds, shook on orbital shaker at maximum speed for six minutes, followed by addition of 188 µL LC-MS grade water. Finally, each sample was vortexed for 10 seconds and centrifuged for 2 minutes at 14,000 rpm. The top phase of the biphasic solution was aliquoted into 1.5 mL microcentrifuge tubes for 350 µL aliquots of MTBE phase. Extraction was carried out at 4°C. All extract tubes were dried under vacuum and frozen at -80°C until LC-MS/MS analysis. Lipidomics analysis followed methods of Cajka et al. 2017 (doi: 10.1021/acs.analchem.7b03404). Non-polar lipids were analyzed on Vanquish Focused UHPLC coupled to a Q-Exactive HF mass spectrometer (ThermoFisher Scientific). Liquid chromatography used a Waters Acquity UPLC CSH C18 column (100mm x 2.1mm, 1.7 μm particle size) coupled to an Acquity UPLC CSH C18 VanGuard precolumn (5 x 2.1 mm; 1.7 μm) (Waters, Milford, MA) with mobile phases of 60:40 (v/v) acetonitrile/ water, and 90:10 (v/v) isopropanol/acetonitrile, both of which had 10 mM ammonium formate and 0.1% formic acid for positive mode ionization analysis, and 10 mM ammonium acetate and 0.1% acetic acid for negative mode ionization analysis. Three and five microliters of reconstituted sample were injected onto column for positive and negative mode ionization analysis respectively. Mobile phase gradient was identical to that of Cajka et al. Data were collected in data dependent manner with the top four ions from each MS1 scan being selected for MS/MS fragmentation. A scan range from 120 to 1200 m/z was used for this analysis. Samples were analyzed in a randomized order with a method blank and quality control plasma sample analyzed between every ten samples.

Combined analysis:

Analysis ID	AN002100	AN002101
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish Focused UHPLC	Thermo Vanquish Focused UHPLC
Column	Waters Acquity CSH C18 (100 x 2.1mm,1.7um)	Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive HF hybrid Orbitrap	Thermo Q Exactive HF hybrid Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	Peak Height (Normalized Intensity)	Peak Height (Normalized Intensity)

Chromatography:

Chromatography ID:	CH001533
Chromatography Summary:	CSH C18 column run in Positive and Negative modes separately.
Instrument Name:	Thermo Vanquish Focused UHPLC
Column Name:	Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:	65
Flow Gradient:	0 min 15% (B); 0−2 min 30% (B); 2−2.5 min 48% (B); 2.5−11 min 82% (B); 11−11.5 min 99% (B); 11.5−12 min 99% (B); 12−12.1 min 15% (B); and 12.1−15 min 15% (B)
Flow Rate:	0.6 mL/min
Internal Standard:	CE(22:1) iSTD Cer(d18:1/17:0) iSTD Cholesterol d7 iSTD CUDA iSTD DG(12:0/12:0/0:0) iSTD DG(18:1/2:0/0:0) iSTD LPC(17:0) iSTD LPE(17:1) iSTD MG(17:0/0:0/0:0) iSTD PC(12:0/13:0) iSTD PE(17:0/17:0) iSTD SM(d18:1/17:0) iSTD Sphingosine(d17:1) iSTD TG d5(17:0/17:1/17:0) iSTD iSTD Ceramide (d18:1/17:0) iSTD Ceramide (d18:1/17:0) iSTD CUDA iSTD FA d3 (16:0) iSTD LPC (17:0) iSTD LPE (17:1) iSTD MAG (17:0/0:0/0:0) iSTD PC (12:0/13:0) iSTD PE (17:0/17:0) iSTD PG (17:0/17:0) iSTD SM (d18:1/17:0)
Sample Injection:	3uL (negative) 5uL (positive)
Solvent A:	60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:	90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Washing Buffer:	100% IPA
Target Sample Temperature:	4
Chromatography Type:	Reversed phase

MS:

MS ID:	MS001951
Analysis ID:	AN002100
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data were processed using open source software MS-DIAL version 2.82.MS-DIAL performed baseline correction, deconvolution, peak detection, alignment, gap filling, adduct identification, accurate mass/ retention time (m/z-RT) library matching, and MS/MS library matching. MS-DIAL parameters were set to 10 for minimum peak width, 10000 for minimum peak height, MS/MS fragmentation match to library of at least 80%, MS1 tolerance of 0.005 Da, MS2 tolerance of 0.01 Da, smoothing level of 3, and retention time window of 0.15 minutes for retention time matching to an in-house m/z-RT library developed from authentic standards. Tandem MS spectra were matched to library spectra from the Mass Bank of North America (MoNA), NIST17, and LipidBlast.[20] Features that appeared in method blanks were removed from further investigation. Duplicate peaks, isotopes, and adducts were investigated and removed using Mass Spectral Feature List Optimizer.[21] Manual inspection of each annotated compound was conducted to confirm m/z-RT library match, and/or MS/MS library match. Peak height was used as mass spectral intensity at a specific retention time for each annotated lipid. After data processing, each sample was normalized to the total summed intensity of all known features (excluding internal standards).
Ion Mode:	POSITIVE
Collision Energy:	NCE 20.30.40
Ionization:	Positive
Scan Range Moverz:	120-1200
Scanning Cycle:	Top 4 ions selected for MS/MS

MS ID:	MS001952
Analysis ID:	AN002101
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data were processed using open source software MS-DIAL version 2.82.MS-DIAL performed baseline correction, deconvolution, peak detection, alignment, gap filling, adduct identification, accurate mass/ retention time (m/z-RT) library matching, and MS/MS library matching. MS-DIAL parameters were set to 10 for minimum peak width, 10000 for minimum peak height, MS/MS fragmentation match to library of at least 80%, MS1 tolerance of 0.005 Da, MS2 tolerance of 0.01 Da, smoothing level of 3, and retention time window of 0.15 minutes for retention time matching to an in-house m/z-RT library developed from authentic standards. Tandem MS spectra were matched to library spectra from the Mass Bank of North America (MoNA), NIST17, and LipidBlast.[20] Features that appeared in method blanks were removed from further investigation. Duplicate peaks, isotopes, and adducts were investigated and removed using Mass Spectral Feature List Optimizer.[21] Manual inspection of each annotated compound was conducted to confirm m/z-RT library match, and/or MS/MS library match. Peak height was used as mass spectral intensity at a specific retention time for each annotated lipid. After data processing, each sample was normalized to the total summed intensity of all known features (excluding internal standards).
Ion Mode:	NEGATIVE
Collision Energy:	NCE 20.30.40
Ionization:	Negative
Scan Range Moverz:	120-1200
Scanning Cycle:	Top 4 ions selected for MS/MS