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.

Study ID	ST001154
Study Title	A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the International Mouse Phenotyping Consortium
Study Summary	Untargeted 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
Department	Genome Center
Laboratory	West Coast Metabolomics Center
Last Name	Barupal
First Name	Dinesh
Address	451 East Health Science Drive
Email	dinkumar@ucdavis.edu
Phone	5309794354
Submit Date	2019-03-12
Num Groups	31
Total Subjects	220
Num Males	110
Num Females	110
Raw Data Available	Yes
Raw Data File Type(s)	cdf, raw(Thermo), mzML
Analysis Type Detail	GC/LC-MS
Release Date	2019-04-12
Release Version	1

Select appropriate tab below to view additional metadata details:

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	Ion trap	Ion trap
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

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:	Ion trap
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:	Ion trap
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