Summary of Study ST001154

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 PR000773. The data can be accessed directly via it's Project DOI: 10.21228/M8RT1C 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 IDST001154
Study TitleA comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the International Mouse Phenotyping Consortium
Study SummaryUntargeted and targeted metabolomics datasets were acquired for blood plasma samples of 30 mouse knockouts within the International Mouse Phenotyping Consortium (IMPC). http://www.mousephenotype.org/. West Coast Metabolomics Center at UC Davis (https://metabolomics.ucdavis.edu/) conducted the metabolomics analyses.
Institute
University of California, Davis
DepartmentGenome Center
LaboratoryWest Coast Metabolomics Center
Last NameBarupal
First NameDinesh
Address451 East Health Science Drive
Emaildinkumar@ucdavis.edu
Phone5309794354
Submit Date2019-03-12
Num Groups31
Total Subjects220
Num Males110
Num Females110
Raw Data AvailableYes
Raw Data File Type(s)cdf, raw(Thermo), mzML
Analysis Type DetailGC-MS/LC-MS
Release Date2019-04-12
Release Version1
Dinesh Barupal Dinesh Barupal
https://dx.doi.org/10.21228/M8RT1C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000773
Project DOI:doi: 10.21228/M8RT1C
Project Title:A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the International Mouse Phenotyping Consortium
Project Type:Observational study
Project Summary:Untargeted and targeted metabolomics datasets were acquired for blood plasma samples of 30 mouse knockouts and the wildtype strain within the International Mouse Phenotyping Consortium (IMPC http://www.mousephenotype.org/). West Coast Metabolomics Center at UC Davis (https://metabolomics.ucdavis.edu/) conducted the metabolomics analyses.
Institute:University of California, Davis
Department:Genome Center
Last Name:Barupal
First Name:Dinesh
Address:451 Health Science Drive, West Coast Metabolomics Center, Davis, California, 95616, USA
Email:dinkumar@ucdavis.edu
Phone:5309794354

Subject:

Subject ID:SU001238
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:Adult
Gender:Male and female

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA081280215989_027A2m
SA081281204770_025A2m
SA081282216077_028A2m
SA081283204771_026A2m
SA081284216079_029A2m
SA081285216080_030A2m
SA081286190365_065Ahcy
SA081287190372_066Ahcy
SA081288181061_064Ahcy
SA081289180957_062Ahcy
SA081290180958_063Ahcy
SA081291180956_061Ahcy
SA081292123951_017Atp5b
SA081293144064_016Atp5b
SA081294123953_018Atp5b
SA081295143866_013Atp5b
SA081296143869_015Atp5b
SA081297143867_014Atp5b
SA081298296501_122Atp6v0d1
SA081299296503_123Atp6v0d1
SA081300254467_124Atp6v0d1
SA081301254470_126Atp6v0d1
SA081302254468_125Atp6v0d1
SA081303296500_121Atp6v0d1
SA081304224106_041C8a
SA081305222899_040C8a
SA081306257445_039C8a
SA081307257443_038C8a
SA081308224107_042C8a
SA081309233525_037C8a
SA081310217741_113Cdk4
SA081311206819_112Cdk4
SA081312206925_110Cdk4
SA081313206923_109Cdk4
SA081314217742_114Cdk4
SA081315209532_111Cdk4
SA081316125374_053Dhfr
SA081317129283_049Dhfr
SA081318122070_052Dhfr
SA081319129286_051Dhfr
SA081320129285_050Dhfr
SA081321125375_054Dhfr
SA081322424983_127Dync1li1
SA081323447116_132Dync1li1
SA081324447115_131Dync1li1
SA081325428092_130Dync1li1
SA081326424984_128Dync1li1
SA081327427987_129Dync1li1
SA081328410985_088G6pd2
SA081329430037_089G6pd2
SA081330432863_090G6pd2
SA081331420424_085G6pd2
SA081332429932_086G6pd2
SA081333429948_087G6pd2
SA08133443709_043Galc
SA08133540494_047Galc
SA08133643712_045Galc
SA08133740393_046Galc
SA08133843711_044Galc
SA08133940495_048Galc
SA08134038379_094Gnpda1
SA08134140790_095Gnpda1
SA08134240681_092Gnpda1
SA08134340793_096Gnpda1
SA08134438276_091Gnpda1
SA08134540683_093Gnpda1
SA081346190701_012Idh1
SA081347138120_011Idh1
SA081348138110_010Idh1
SA081349115996_009Idh1
SA081350115900_008Idh1
SA081351185262_007Idh1
SA081352435798_023Iqgap1
SA081353487667_024Iqgap1
SA081354506107_022Iqgap1
SA081355493977_021Iqgap1
SA081356487464_019Iqgap1
SA081357487461_020Iqgap1
SA081358111495_100Lmbrd1
SA08135985376_099Lmbrd1
SA08136072465_097Lmbrd1
SA081361118598_101Lmbrd1
SA08136285374_098Lmbrd1
SA081363118599_102Lmbrd1
SA081364225110_035Mfap4
SA081365212480_032Mfap4
SA081366225109_034Mfap4
SA081367212477_031Mfap4
SA081368225111_036Mfap4
SA081369213386_033Mfap4
SA081370356268_074Mmachc
SA081371356157_073Mmachc
SA081372356272_075Mmachc
SA081373356371_076Mmachc
SA081374356475_077Mmachc
SA081375356477_078Mmachc
SA081376349944_156Mvk
SA081377328199_155Mvk
SA081378328195_154Mvk
SA081379345321_152Mvk
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 220

Collection:

Collection ID:CO001232
Collection Summary:Blood specimens were collected using the IMPC protocol https://www.mousephenotype.org/impress/
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001253
Treatment Summary:30 genotypes and one group of wildtype mouse

Sample Preparation:

Sampleprep ID:SP001246
Sampleprep Summary:Metabolites were extracted using standard protocols for GCMS and LCMS assays by the West Coast Metabolomics Center.

Combined analysis:

Analysis ID AN001941 AN001942 AN001943 AN001944 AN001945 AN001946 AN001947
Analysis type MS MS MS MS MS MS MS
Chromatography type GC Reversed phase Reversed phase HILIC HILIC Reversed phase Reversed phase
Chromatography system Agilent 6890N Thermo Vanquish Thermo Vanquish Thermo Vanquish Thermo Vanquish Waters Acquity I-Class Waters Acquity I-Class
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH C18 (100 x 2mm,1.7um) Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type EI ESI ESI ESI ESI ESI ESI
MS instrument type GC-TOF Orbitrap Orbitrap Orbitrap Orbitrap Triple quadrupole Triple quadrupole
MS instrument name Leco Pegasus IV TOF Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap ABI Sciex 6500 QTrap ABI Sciex 6500 QTrap
Ion Mode NEGATIVE POSITIVE NEGATIVE POSITIVE NEGATIVE UNSPECIFIED NEGATIVE
Units normalized peak height normalized peak height normalized peak height normalized peak height normalized peak height nM nM

Chromatography:

Chromatography ID:CH001408
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC
  
Chromatography ID:CH001409
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Flow Gradient:0 min 85% (A); 0-2 min 70% (A); 2-2.5 min 52% (A); 2.5-11 min 18% (A); 11-11.5 min 1% (A); 11.5-12 min 1% (A); 12-12.1 min 85% (A); 12.1-15 min 85% (A)
Solvent A:Pos mode:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate, Neg mode:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium acetate
Solvent B:Pos mode:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate, Neg mode:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium acetate
Chromatography Type:Reversed phase
  
Chromatography ID:CH001410
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:100% (B) for 2 min, 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min and isocratic until 16.75 min.
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate
Solvent B:95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate
Chromatography Type:HILIC
  
Chromatography ID:CH001411
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:45
Flow Gradient:The 20 min gradient is: 0-0.5 min 10% B, 0.5-1 min 10-20% B, 1-1.5 min 20-22.5% B, 1.5-11 min 22.5-45% B, 11-12.5 min 45-95% B, 12.5-16 min 95% B, 16-16.5 min 95-10% B, 16.5-20 min 10% B
Flow Rate:400 µL/min
Solvent A:100% water; 0.1% formic acid;
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001412
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:45
Flow Gradient:16 min gradient is: 0-1 min 25-40% B, 1-2.5 min 40-42% B, 2.5-4.5 min 42-50% B, 4.5-10.5 min 50-65% B, 10.5-12.5 min 65-75% B, 12.5-14 min 75-85% B, 14-14.5 min 85-95% B, 14.5-15 min 95-25% B, 15-16 min 25% B.
Flow Rate:250 µL/min
Solvent A:100% water; 0.1% acetic acid
Solvent B:90% acetonitrile/10% isopropanol; 0.1% acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS001797
Analysis ID:AN001941
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:Data acquisition : An Agilent 6890 gas chromatography instrument equipped with a Gerstel automatic linear exchange systems (ALEX) which included a multipurpose sample dual rail and a Gerstel cold injection system (CIS). The CIS temperature program was : 50°C to 275°C final temperature at a rate of 12 °C/s and hold for 3 minutes. Injection volume was 0.5 µL with 10 µL/s injection speed. Injection mode was splitless with a purge time of 25 seconds. Injector liner was changed after every 10 samples. Injection syringe was washed with 10 µL of ethyl acetate before and after each run. A Rtx-5Sil MS column (30m length, 0.25 mm i.d, 0.25 microM 95% dimethyl 5% diphenyl polysiloxane film). An additional 10 m integrated guard column was used. Mobile phase was 99.9999% pure Helium gas with a flow rate of 1ml/min. GC temperature program was : hold at 50°C for 1 min, ramped at 20°C/min to 330°C and then hold for 5 minutes. A Leco Pegasus IV time of flight mass spectrometer was used to acquire data. The transfer line temperature between gas chromatograph and mass spectrometer was set to 280°C. Electron impact ionization at 70V was employed with an ion-source temperature of 250°C. Acquisition rate was 17 spectra/second with a scan mass range of 85-500 Da. Data processing : Data processing Raw data files are preprocessed directly after data acquisition and stored as ChromaTOF-specific *.peg files, as generic *.txt result files and additionally as generic ANDI MS *.cdf files. ChromaTOF vs. 4.0 is used for data preprocessing without smoothing, 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise levels of 5:1 throughout the chromatogram. Apex masses are reported for use in the BinBase algorithm. Result *.txt files are exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics BinBase database.The BinBase algorithm (rtx5) used the settings: validity of chromatogram (10^7 counts s -1 ), unbiased retention index marker detection (MS similarity>800, validity of intensity range for high m/z marker ions), retention index calculation by 5th order polynomial regression. Spectra are cut to 5% base peak abundance and matched to database entries from most to least abundant spectra using the following matching filters: retention index window ±2,000 units (equivalent to about ±2 s retention time), validation of unique ions and apex masses (unique ion must be included in apexing masses and present at >3% of base peak abundance), mass spectrum similarity must fit criteria dependent on peak purity and signal/noise ratios and a final isomer filter. Failed spectra are automatically entered as new database entries if s/n >25, purity 80%. All thresholds reflect settings for ChromaTOF v. 4.0. Quantification is reported as peak height using the unique ion as default, unless a different quantification ion is manually set in the BinBase administration software BinView. A quantification report table is produced for all database entries that are positively detected in more than 10% of the samples of a study design class (as defined in the miniX database) for unidentified metabolites. A subsequent post-processing module is employed to automatically replace missing values from the *.cdf files. Replaced values are labeled as ‘low confidence’ by color coding, and for each metabolite, the number of high-confidence peak detections is recorded as well as the ratio of the average height of replaced values to high-confidence peak detections. These ratios and numbers are used for manual curation of automatic report data sets to data sets released for submission.
Ion Mode:NEGATIVE
  
MS ID:MS001798
Analysis ID:AN001942
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data acquisition : Extracted lipids were separated on an Acquity UPLC CSH C18 column (100 x 2.1 mm; 1.7 µm) maintained at 65°C. The mobile phases for positive mode consisted of 60:40 acetonitrile:water with 10 mM ammonium formate and 0.1% formic acid (A) and 90:10 isopropanol:acetonitrile with 10 mM ammonium formate and 0.1% formic acid (B). For negative mode, the mobile phase modifier was 10 mM ammonium acetate instead. The gradient was as follows: 0 min 85% (A); 0–2 min 70% (A); 2–2.5 min 52% (A); 2.5–11 min 18% (A); 11–11.5 min 1% (A); 11.5–12 min 1% (A); 12–12.1 min 85% (A); 12.1–15 min 85% (A). Sample temperature is maintained at 4°C in the autosampler. 2 µL of sample was injected. Vanquish UHPLC system (ThermoFisher Scientific) was used. Thermo Q-Exactive HF Orbitrap MS instrument was operated in electrospray ionization (ESI) in positive and negative modes respectively with the following parameters: mass range 120−1700 m/z; spray voltage 3.6kV (ESI+) and -3kV (ESI-), sheath gas (nitrogen) flow rate 60 units; auxiliary gas (nitrogen) flow rate 25 units, capillary temperature 320 °C, full scan MS1 mass resolving power 60,000, data-dependent MS/MS (dd-MS/MS) 4 scans per cycle, normalized collision energy at 20%, 30% and 40%, dd-MS/MS mass resolving power 15,000. Thermo Xcalibur 4.0.27.19 was used for data acquisition and analysis. Instruments was tuned by manufacturer’s recommendations. Data processing : Raw data files were converted to the mzML format using the ProteoWizard MSConvert utility. For each m/z values ion chromatogram was extracted with m/z thresholds of 0.005 dalton and retention time threshold of 0.10 minute. Apex of the extracted ion chromatograph was used as peak height value and exported to a txt file. Peak height files for all the samples were merged together to generate a data matrix. Targeted peak height signal extraction was performed using an R script .Extracted ion chromatograms for each peak were saved as pictures. CSH-POS and CSH-NEG data matrices were generated. No normalization was applied as minimum signal drift was observed during analysis.
Ion Mode:POSITIVE
  
MS ID:MS001799
Analysis ID:AN001943
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data acquisition : Extracted lipids were separated on an Acquity UPLC CSH C18 column (100 x 2.1 mm; 1.7 µm) maintained at 65°C. The mobile phases for positive mode consisted of 60:40 acetonitrile:water with 10 mM ammonium formate and 0.1% formic acid (A) and 90:10 isopropanol:acetonitrile with 10 mM ammonium formate and 0.1% formic acid (B). For negative mode, the mobile phase modifier was 10 mM ammonium acetate instead. The gradient was as follows: 0 min 85% (A); 0–2 min 70% (A); 2–2.5 min 52% (A); 2.5–11 min 18% (A); 11–11.5 min 1% (A); 11.5–12 min 1% (A); 12–12.1 min 85% (A); 12.1–15 min 85% (A). Sample temperature is maintained at 4°C in the autosampler. 2 µL of sample was injected. Vanquish UHPLC system (ThermoFisher Scientific) was used. Thermo Q-Exactive HF Orbitrap MS instrument was operated in electrospray ionization (ESI) in positive and negative modes respectively with the following parameters: mass range 120−1700 m/z; spray voltage 3.6kV (ESI+) and -3kV (ESI-), sheath gas (nitrogen) flow rate 60 units; auxiliary gas (nitrogen) flow rate 25 units, capillary temperature 320 °C, full scan MS1 mass resolving power 60,000, data-dependent MS/MS (dd-MS/MS) 4 scans per cycle, normalized collision energy at 20%, 30% and 40%, dd-MS/MS mass resolving power 15,000. Thermo Xcalibur 4.0.27.19 was used for data acquisition and analysis. Instruments was tuned by manufacturer’s recommendations. Data processing : Raw data files were converted to the mzML format using the ProteoWizard MSConvert utility. For each m/z values ion chromatogram was extracted with m/z thresholds of 0.005 dalton and retention time threshold of 0.10 minute. Apex of the extracted ion chromatograph was used as peak height value and exported to a txt file. Peak height files for all the samples were merged together to generate a data matrix. Targeted peak height signal extraction was performed using an R script. Extracted ion chromatograms for each peak were saved as pictures. CSH-POS and CSH-NEG data matrices were generated. No normalization was applied as minimum signal drift was observed during analysis.
Ion Mode:NEGATIVE
  
MS ID:MS001800
Analysis ID:AN001944
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data acquisition : 3 µL sample aliquots were injected on a Waters Acquity UPLC BEH Amide column (150 mm length × 2.1 mm id; 1.7 μm particle size) maintained at 45°C. A Waters Acquity VanGuard BEH Amide pre-column (5 mm × 2.1 mm id; 1.7 μm particle size) was used as guard column. Mobile phase A was 100% LC-MS grade water with 10 mM ammonium formate and 0.125% formic acid and mobile phase B was 95:5 v/v acetonitrile:water with 10 mM ammonium formate and 0.125% formic acid. Gradient was started at 100% (B) for 2 min, 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min and isocratic until 16.75 min. The column flow was 0.4 mL/min. Vanquish UHPLC system (ThermoFisher Scientific) was used. A Thermo Q-Exactive HF Orbitrap MS instrument was operated in electrospray ionization (ESI) in positive and negative modes respectively with the following parameters: mass range 60−900 m/z; spray voltage 3.6kV (ESI+) and -3kV (ESI-), sheath gas (nitrogen) flow rate 60 units; auxiliary gas (nitrogen) flow rate 25 units, capillary temperature 320°C, full scan MS1 mass resolving power 60,000, data-dependent MSMS (dd-MSMS) 4 scans per cycle, normalized collision energy at 20%, 30% and 40%, dd-MSMS mass resolving power 15,000. Thermo Xcalibur 4.0.27.19 was used for data acquisition and analysis. Instruments was tuned by manufacturer’s recommendations. Data processing : Raw data files were converted to the mzML format using the ProteoWizard MSConvert utility. For each m/z values ion chromatogram was extracted with m/z thresholds of 0.005 dalton and retention time threshold of 0.10 minute. Apex of the extracted ion chromatograph was used as peak height value and exported to a txt file. Peak height files for all the samples were merged together to generate a data matrix. Targeted peak height signal extraction was performed using an R script. Extracted ion chromatograms for each peak were saved as pictures. HILIC-POS data were not normalized because no batch effect was observed. HILIC-NEG data were normalized by the median value for each batch to remove batch effects.
Ion Mode:POSITIVE
  
MS ID:MS001801
Analysis ID:AN001945
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data acquisition : 3 µL sample aliquots were injected on a Waters Acquity UPLC BEH Amide column (150 mm length × 2.1 mm id; 1.7 μm particle size) maintained at 45°C. A Waters Acquity VanGuard BEH Amide pre-column (5 mm × 2.1 mm id; 1.7 μm particle size) was used as guard column. Mobile phase A was 100% LC-MS grade water with 10 mM ammonium formate and 0.125% formic acid and mobile phase B was 95:5 v/v acetonitrile:water with 10 mM ammonium formate and 0.125% formic acid. Gradient was started at 100% (B) for 2 min, 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min and isocratic until 16.75 min. The column flow was 0.4 mL/min. Vanquish UHPLC system (ThermoFisher Scientific) was used. A Thermo Q-Exactive HF Orbitrap MS instrument was operated in electrospray ionization (ESI) in positive and negative modes respectively with the following parameters: mass range 60−900 m/z; spray voltage 3.6kV (ESI+) and -3kV (ESI-), sheath gas (nitrogen) flow rate 60 units; auxiliary gas (nitrogen) flow rate 25 units, capillary temperature 320°C, full scan MS1 mass resolving power 60,000, data-dependent MSMS (dd-MSMS) 4 scans per cycle, normalized collision energy at 20%, 30% and 40%, dd-MSMS mass resolving power 15,000. Thermo Xcalibur 4.0.27.19 was used for data acquisition and analysis. Instruments was tuned by manufacturer’s recommendations. Data processing : Raw data files were converted to the mzML format using the ProteoWizard MSConvert utility. For each m/z values ion chromatogram was extracted with m/z thresholds of 0.005 dalton and retention time threshold of 0.10 minute. Apex of the extracted ion chromatograph was used as peak height value and exported to a txt file. Peak height files for all the samples were merged together to generate a data matrix. Targeted peak height signal extraction was performed using an R script. Extracted ion chromatograms for each peak were saved as pictures. HILIC-POS data were not normalized because no batch effect was observed. HILIC-NEG data were normalized by the median value for each batch to remove batch effects.
Ion Mode:NEGATIVE
  
MS ID:MS001802
Analysis ID:AN001946
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:For bile acids and steroids, reverse-phase liquid chromatography was achieved on a Waters Acquity BEH C18 column (1.7 µm, 2.1x100 mm) with its corresponding Vanguard precolumn at 45 °C at a flow rate of 400 µL/min. Mobile phase A was LC-MS grade water with 0.1% formic acid; mobile phase B was acetonitrile with 0.1% formic acid. The 20 min gradient is: 0–0.5 min 10% B, 0.5–1 min 10-20% B, 1–1.5 min 20-22.5% B, 1.5–11 min 22.5-45% B, 11–12.5 min 45-95% B, 12.5–16 min 95% B, 16–16.5 min 95-10% B, 16.5–20 min 10% B.Extracts were analyzed by liquid chromatography (Waters ACQUITY UPLC I-Class system) coupled to a Sciex 6500+ QTRAP hybrid, triple quadrupole linear ion trap mass spectrometer. 5 µL of each extract was injected. Scheduled multiple reaction monitoring (MRM) was performed with optimized collision energies, de-clustering potentials, and collision cell exit potentials for individual analyte. A LC-MRM targeted method was used to analyze both bile acids and steroids with positive and negative polarity switching. Oxylipins were analyzed in another LC-MRM method in negative ionization mode. All analytes were quantified against 6-point calibration curves using internal standards. Turbo Spray Ion Source parameters are: curtain gas (CUR) 25 psi, nebulizer gas (GS1) 50 psi, turbo-gas (GS2) 50 psi, electrospray voltage −4.5 kV/+3 kV, and source temperature 525 °C. Nitrogen was used as the collision gas. Software Analyst 1.6.3 and MultiQuant 3.0.2 (AB Sciex) were used for data acquisition and quantification.
Ion Mode:UNSPECIFIED
  
MS ID:MS001803
Analysis ID:AN001947
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:For oxylipins, LC separation was conducted on the same column but mobile phase A was water with 0.1% acetic acid and B was acetonitrile:isopropanol 90:10 (v/v) with 0.1% acetic acid. Column is maintained at 45 °C at the flow rate of 250 µL/min. The 16 min gradient is: 0–1 min 25-40% B, 1–2.5 min 40-42% B, 2.5–4.5 min 42-50% B, 4.5–10.5 min 50-65% B, 10.5–12.5 min 65-75% B, 12.5–14 min 75-85% B, 14–14.5 min 85-95% B, 14.5–15 min 95-25% B, 15–16 min 25% B. Extracts were analyzed by liquid chromatography (Waters ACQUITY UPLC I-Class system) coupled to a Sciex 6500+ QTRAP hybrid, triple quadrupole linear ion trap mass spectrometer. 5 µL of each extract was injected. Scheduled multiple reaction monitoring (MRM) was performed with optimized collision energies, de-clustering potentials, and collision cell exit potentials for individual analyte. A LC-MRM targeted method was used to analyze both bile acids and steroids with positive and negative polarity switching. Oxylipins were analyzed in another LC-MRM method in negative ionization mode. All analytes were quantified against 6-point calibration curves using internal standards. Turbo Spray Ion Source parameters are: curtain gas (CUR) 25 psi, nebulizer gas (GS1) 50 psi, turbo-gas (GS2) 50 psi, electrospray voltage −4.5 kV/+3 kV, and source temperature 525 °C. Nitrogen was used as the collision gas. Software Analyst 1.6.3 and MultiQuant 3.0.2 (AB Sciex) were used for data acquisition and quantification.
Ion Mode:NEGATIVE
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