Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA164995

Local Sample ID:	PD1074 C. elegans mixture 2
Subject ID:	SU001854
Subject Type:	Synthetic sample

Select appropriate tab below to view additional metadata details:

Subject:

Subject ID:	SU001854
Subject Type:	Synthetic sample

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
PD1074 C. elegans mixture 2	SA164995	FL019741	AGC 5e4 - R 240K - neg	Experimental Condition

Collection:

Collection ID:	CO001847
Collection Summary:	PD1074 C. elegans samples (~10 mg) were collected and lyophilized.
Sample Type:	Worms
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001867
Treatment Summary:	standard PD1047 C.elegans treatment

Sample Preparation:

Sampleprep ID:	SP001860
Sampleprep Summary:	Model Mixture Sample Preparation One hundred and four selected chemical standard compounds were purchased from Sigma-Aldrich (St. Louis, MO, USA) and used to prepare stock solutions at a concentration of 0.001 M in LC-MS grade methanol (Fisher Scientific, Pittsburgh, PA, USA). These standards were selected because they map to key metabolic pathways, some involved in cancer. If a chemical could not be completely dissolved in methanol, LC-MS grade water (Fisher Scientific, Pittsburgh, PA, USA) was added to increase solubility. A pooled sample of 104 standard compounds was diluted with methanol at a final concentration of 5 μM. PD1074 C. elegans Bio-mixture Sample Preparation Three 2.0 mm zirconium oxide beads and ~75 μL volume of 0.5 mm glass beads were added to each lyophilized PD1074 C. elegans sample (~10 mg). Samples were placed in a TissueLyser II (QIAGEN, Hilden, Germany) and homogenized at 1,800 rpm, -80 °C for 3 min. One and a half mL of 80% methanol (in water) was added to each homogenized sample. Samples were then shaken using an Isotemp high speed shaker (Fisher Scientific, Pittsburgh, PA, USA) at 1,500 rpm for 30 min, and centrifuged at 22,100 g for 5 min. The supernatant was collected, dried and stored at -80 °C. Prior to MS analysis, dried C. elegans matrices were resuspended with 1 mL LC-MS grade methanol containing the 104 standard compounds at a 5 μM concentration.

Sampleprep ID:

SP001860

Sampleprep Summary:

Model Mixture Sample Preparation One hundred and four selected chemical standard compounds were purchased from Sigma-Aldrich (St. Louis, MO, USA) and used to prepare stock solutions at a concentration of 0.001 M in LC-MS grade methanol (Fisher Scientific, Pittsburgh, PA, USA). These standards were selected because they map to key metabolic pathways, some involved in cancer. If a chemical could not be completely dissolved in methanol, LC-MS grade water (Fisher Scientific, Pittsburgh, PA, USA) was added to increase solubility. A pooled sample of 104 standard compounds was diluted with methanol at a final concentration of 5 μM. PD1074 C. elegans Bio-mixture Sample Preparation Three 2.0 mm zirconium oxide beads and ~75 μL volume of 0.5 mm glass beads were added to each lyophilized PD1074 C. elegans sample (~10 mg). Samples were placed in a TissueLyser II (QIAGEN, Hilden, Germany) and homogenized at 1,800 rpm, -80 °C for 3 min. One and a half mL of 80% methanol (in water) was added to each homogenized sample. Samples were then shaken using an Isotemp high speed shaker (Fisher Scientific, Pittsburgh, PA, USA) at 1,500 rpm for 30 min, and centrifuged at 22,100 g for 5 min. The supernatant was collected, dried and stored at -80 °C. Prior to MS analysis, dried C. elegans matrices were resuspended with 1 mL LC-MS grade methanol containing the 104 standard compounds at a 5 μM concentration.

Combined analysis:

Analysis ID	AN002884	AN002885
Analysis type	MS	MS
Chromatography type	HILIC	HILIC
Chromatography system	Thermo Vanquish	Thermo Vanquish
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	Orbitrap	Orbitrap
MS instrument name	Thermo Orbitrap ID-X Tribrid	Thermo Orbitrap ID-X Tribrid
Ion Mode	POSITIVE	NEGATIVE
Units	Da	Da

Chromatography:

Chromatography ID:	CH002139
Chromatography Summary:	HILIC method
Instrument Name:	Thermo Vanquish
Column Name:	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:	40
Flow Rate:	0.4 ml/min
Sample Injection:	2μL
Solvent A:	80% water/20% acetonitrile; 0.1% formic acid; 10 mM ammonium acetate
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	HILIC

MS:

MS ID:	MS002677
Analysis ID:	AN002884
Instrument Name:	Thermo Orbitrap ID-X Tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Samples were analyzed in positive and negative ion modes for HILIC chromatography. Spectral features were extracted from the raw data using MZmine 2.51.
Ion Mode:	POSITIVE
Spray Voltage:	3.5 kV
Automatic Gain Control:	5e4, 1e5, 5e5

MS ID:	MS002678
Analysis ID:	AN002885
Instrument Name:	Thermo Orbitrap ID-X Tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Samples were analyzed in positive and negative ion modes for HILIC chromatography. Spectral features were extracted from the raw data using MZmine 2.51.
Ion Mode:	NEGATIVE
Spray Voltage:	-2.5 kV
Automatic Gain Control:	5e4, 1e5, 5e5