Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA214307

Local Sample ID:	Patient_Positive_P-49
Subject ID:	SU002329
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Select appropriate tab below to view additional metadata details:

Subject:

Subject ID:	SU002329
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
Patient_Positive_P-49	SA214307	FL026026	Patient	Group

Collection:

Collection ID:	CO002322
Collection Summary:	Venous blood was drawn in 8.5 mL purple cap Vacutainer EDTA tubes and gently invert to mix. Plasma was collected after centrifugation at 1000 g for 15 min. All samples were immediately aliquoted to Eppendorf tubes and frozen at -80 ºC until analysis.
Sample Type:	Blood (plasma)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002341
Treatment Summary:	NA

Sample Preparation:

Sampleprep ID:	SP002335
Sampleprep Summary:	50 μL plasma, was mixed with 20 μL internal standard working solution (SPLASH® LIPIDOMIX® Mass Spec Standard + Cer/sph mixture I), extracted with 1000 μL butanol/methanol (1/1, v/v, 10 mM ammonium formate) for 10 min on a vortex mixture. Samples were pelleted by centrifugation at 4000 x g for 5 min at room temperature. The supernatant was moved to a clean glass tube, dried under nitrogen, and resuspended in 100 μL MTBE/methanol (1/3, v/v) with 10 mM ammonium formate. 5 μL of each sample was combined to make a pooled quality control (QC) sample and ran every ten samples in the long sequence to monitor retention time and signal intensity drift. The remaining samples (50 μL) were transferred into injection vials for lipidomic analysis.

Sampleprep ID:

SP002335

Sampleprep Summary:

50 μL plasma, was mixed with 20 μL internal standard working solution (SPLASH® LIPIDOMIX® Mass Spec Standard + Cer/sph mixture I), extracted with 1000 μL butanol/methanol (1/1, v/v, 10 mM ammonium formate) for 10 min on a vortex mixture. Samples were pelleted by centrifugation at 4000 x g for 5 min at room temperature. The supernatant was moved to a clean glass tube, dried under nitrogen, and resuspended in 100 μL MTBE/methanol (1/3, v/v) with 10 mM ammonium formate. 5 μL of each sample was combined to make a pooled quality control (QC) sample and ran every ten samples in the long sequence to monitor retention time and signal intensity drift. The remaining samples (50 μL) were transferred into injection vials for lipidomic analysis.

Combined analysis:

Analysis ID	AN003661	AN003662
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000
Column	Thermo Accucore C18 (100 x 2.1mm,2.6um)	Thermo Accucore C18 (100 x 2.1mm,2.6um)
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	intensity	intensity

Chromatography:

Chromatography ID:	CH002713
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Thermo Accucore C18 (100 x 2.1mm,2.6um)
Column Temperature:	35
Flow Gradient:	0 min, 90% A; 1 min, 90% A; 4 min, 60% A; 12 min, 25% A; 21 min, 1% A; 24 min, 1% A; 24.1 min, 90% A; 28 min, 90%.
Flow Rate:	0.4 ml/min
Injection Temperature:	4
Solvent A:	50% acetonitrile/50% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:	10% acetonitrile/88% isopropanol/2% water; 0.02% formic acid; 2 mM ammonium formate
Analytical Time:	28min
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003412
Analysis ID:	AN003661
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Samples were analyzed using a Q Exactive HF (QE-HF) (Thermo Scientific, Waltham, MA) equipped with a heated electro-spray ionization (HESI) source operated in both positive and negative ion mode. For DDA library generation (untargeted lipidomics), data acquisition was performed on the pooled QC samples in Full Scan/ddMS2 mode @ 120,000 resolutions. The Full Scan settings as follows: AGC target = 1e6; Maximum IT = 250 ms; scan range = 250 to 1800 m/z. Top 20 MS/MS spectral (dd-MS2) @ 15000 were generated with AGC target = 1e5, Maximum IT=25 ms, and (N)CE/stepped nce = 20, 30, 40v. For untargeted lipid analysis, LipidSearch 4.2 (Thermo Scientific, Waltham, MA) was used for peak detection, identification, alignment, and quantification. Well annotated lipids (MS spectral match) were used to generate a inclusion list (Supplementary Table 4) for targeted lipidomics analysis. Targeted lipidomics were performed in Full scan + PRM modes. The PRM settings were as follows: resolution = 15000, AGC target = 2e5, Maximum IT=25 ms, loop count = 36, isolation window = 2.0, (N)CE was optimized for each lipid class.
Ion Mode:	POSITIVE

MS ID:	MS003413
Analysis ID:	AN003662
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Samples were analyzed using a Q Exactive HF (QE-HF) (Thermo Scientific, Waltham, MA) equipped with a heated electro-spray ionization (HESI) source operated in both positive and negative ion mode. For DDA library generation (untargeted lipidomics), data acquisition was performed on the pooled QC samples in Full Scan/ddMS2 mode @ 120,000 resolutions. The Full Scan settings as follows: AGC target = 1e6; Maximum IT = 250 ms; scan range = 250 to 1800 m/z. Top 20 MS/MS spectral (dd-MS2) @ 15000 were generated with AGC target = 1e5, Maximum IT=25 ms, and (N)CE/stepped nce = 20, 30, 40v. For untargeted lipid analysis, LipidSearch 4.2 (Thermo Scientific, Waltham, MA) was used for peak detection, identification, alignment, and quantification. Well annotated lipids (MS spectral match) were used to generate a inclusion list (Supplementary Table 4) for targeted lipidomics analysis. Targeted lipidomics were performed in Full scan + PRM modes. The PRM settings were as follows: resolution = 15000, AGC target = 2e5, Maximum IT=25 ms, loop count = 36, isolation window = 2.0, (N)CE was optimized for each lipid class.
Ion Mode:	NEGATIVE