Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA151259

Local Sample ID:	23 T_076
Subject ID:	SU001718
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

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Subject:

Subject ID:	SU001718
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
23 T_076	SA151259	FL017693	tumor	Sample Source

Collection:

Collection ID:	CO001711
Collection Summary:	human liver samples were collected to compare tumor versus nontumor
Sample Type:	Liver

Treatment:

Treatment ID:	TR001731
Treatment Summary:	comparison of tumor versus nontumor patients

Sample Preparation:

Sampleprep ID:	SP001724
Sampleprep Summary:	Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization.

Sampleprep ID:

SP001724

Sampleprep Summary:

Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization.

Combined analysis:

Analysis ID	AN002686
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Agilent
Column	Waters ACQUITY UPLC CSH C18
MS Type	EI
MS instrument type	QTOF
MS instrument name	Agilent 6550 QTOF
Ion Mode	POSITIVE
Units	counts per second

Chromatography:

Chromatography ID:	CH001980
Chromatography Summary:	The LC/QTOFMS analyses are performed using an Agilent 1290 Infinity LC system (G4220A binary pump, G4226A autosampler, and G1316C Column Thermostat) coupled to either an Agilent 6530 (positive ion mode) or an Agilent 6550 mass spectrometer equipped with an ion funnel (iFunnel) (negative ion mode). Lipids are separated on an Acquity UPLC CSH C18 column (100 x 2.1 mm; 1.7 µm) maintained at 65°C at a flow-rate of 0.6 mL/min. Solvent pre-heating (Agilent G1316) was used. The mobile phases consist of 60:40 acetonitrile:water with 10 mM ammonium formate and 0.1% formic acid (A) and 90:10 propan-2-ol:acetonitrile with 10 mM ammonium formate and 0.1% formic acid. The gradient is 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). A sample volume of 3 µL is used for the injection. Sample temperature is maintained at 4°C in the autosampler.
Instrument Name:	Agilent
Column Name:	Waters ACQUITY UPLC CSH C18
Column Temperature:	65
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).
Flow Rate:	0.6 mL/min
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
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002485
Analysis ID:	AN002686
Instrument Name:	Agilent 6550 QTOF
Instrument Type:	QTOF
MS Type:	EI
MS Comments:	For the data processing the MassHunter software is used, and a unique ID is given to each lipid based on its retention time and exact mass (RT_mz). This allows the report of peak areas/heights or concentration of lipids based on the use of particular internal standards. Lipids are identified based on their unique MS/MS fragmentation patterns using in-house software, Lipidblast. Using complex lipid class-specific internal standards this approach is used to quantify >400 lipid species including: mono-, di- and triacylglycerols, glycerophospholipids, sphingolipids, cholesterol esters, ceramides, and fatty acids.
Ion Mode:	POSITIVE