Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA125673

Local Sample ID:	13202700
Subject ID:	SU001564
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Age Or Age Range:	18-45
Gender:	Male and female
Human Nutrition:	Low glycemic load and high glycemic load diet
Human Inclusion Criteria:	We recruited non-smoking, healthy individuals between the ages of 18-45 years from the Greater Seattle area.
Human Exclusion Criteria:	Exclusion criteria consisted of impaired fasting glucose (fasting blood glucose ≥5.6 mmol/L), any physician-diagnosed condition requiring a restricted diet, food allergies, regular use of hormones or anti-inflammatory medication, current pregnancy or lactation or plans to become pregnant, or heavy use of alcohol (>2 drinks/d)

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Subject:

Subject ID:	SU001564
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Age Or Age Range:	18-45
Gender:	Male and female
Human Nutrition:	Low glycemic load and high glycemic load diet
Human Inclusion Criteria:	We recruited non-smoking, healthy individuals between the ages of 18-45 years from the Greater Seattle area.
Human Exclusion Criteria:	Exclusion criteria consisted of impaired fasting glucose (fasting blood glucose ≥5.6 mmol/L), any physician-diagnosed condition requiring a restricted diet, food allergies, regular use of hormones or anti-inflammatory medication, current pregnancy or lactation or plans to become pregnant, or heavy use of alcohol (>2 drinks/d)

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
13202700	SA125673	FL015366	LGL	Treatment

Collection:

Collection ID:	CO001559
Collection Summary:	We collected blood at baseline and the end of each 28-d dietary period after a minimum of a 12-h overnight fast. We used a standard protocol to process and store samples at -80°C until analysis. Homeostasis model assessment for insulin resistance (HOMA-IR), which was used as a measure of insulin resistance for our post-hoc analysis, was calculated by dividing the product of fasting insulin and fasting glucose by a normalizing factor. Lipidomics Sample Preparation and Mass Spectrometry Frozen plasma samples were thawed at room temperature (25 °C) for 30 min, vortexed, and 25 µL plasma was transferred to a borosilicate glass culture tube (16 x 100 mm). Next, 0.475 mL water, 1.45 mL 1:0.45 methanol:dichloromethane, and 25 µL isotope-labeled internal standards mixture were added to the tube. The Lipidyzer isotope labeled internal standards mixture consisted of 54 isotopes from 13 lipid classes (Sciex, Framingham, MA). The mixture was vortexed for 5 sec and incubated at room temperature for 30 min. Next, another 0.5 mL water and 0.45 mL dichloromethane were added to the tube, followed by gentle vortexing for 5 sec, and centrifugation at 2500 g at 15 °C for 10 min. The bottom organic layer was transferred to a new tube and 0.9 mL of dichloromethane was added to the original tube for a second extraction. The combined extracts were concentrated under nitrogen and reconstituted in 0.25 mL of the mobile phase (10 mM ammonium acetate in 50:50 methanol:dichloromethane). Quantitative lipidomics was performed with the Sciex Lipidyzer platform consisting of Shimadzu Nexera X2 LC-30AD pumps, a Shimadzu Nexera X2 SIL-30AC autosampler, and a Sciex QTRAP® 5500 mass spectrometer equipped with SelexION® for differential mobility spectrometry (DMS). 1-propanol was used as the chemical modifier for the DMS. Samples were introduced to the mass spectrometer by flow injection at 8 µL/min. Each sample was injected twice, once with the DMS on [phosphatidylcholines (PC); phosphatidylethanolamines (PE); lysophosphatidylcholines (LPC); lysophosphatidylethanolamines (LPE); sphingomyelins (SM)], and once with the DMS off ([cholesterol esters (CE); ceramides (CER); diacylglycerols (DAG); dihydroceramides (DCER)/ free fatty acids(FFA); hexosylceramides (HCER); lactosylceramides (LCER); triacylglycerols (TAG)]. The lipid molecular species were measured using multiple reaction monitoring and positive/negative polarity switching. Positive ion mode detected lipid classes SM, DAG, CE, CER, DCER, HCER, DCER, and TAG, and negative ion mode detected lipid classes LPE, LPC, PC, PE, and FFA. A total of 1070 lipids and fatty acids were targeted in the analysis. Data was acquired and processed using Analyst 1.6.3 and Lipidomics Workflow Manager 1.0.5.0.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR001579
Treatment Summary:	A 7-day rotating menu was created for each diet. At baseline, participants completed a 3-d food record to estimate mean daily calorie intake. Energy intake from the food records along with weight, height, sex and activity level were used to estimate each participant’s daily energy needs necessary to maintain the current weight. The estimated calorie intake was used to adjust the 7-day rotating menu to meet each participant’s needs so that they would remain weight stable during the study. The percentage energy from macronutrients of the two diets were identical: 15% energy from protein, 30% energy from fat, and 55% energy from carbohydrate. The LGL diet provided on average 55 g/d of fiber and 77 g/d of fructose, with a GL of 125 (Table 1). The HGL diet substituted refined grains for whole grains, included other carbohydrates from high-glycemic index food sources and provided on average 28 g/d of fiber and 26 g/d of fructose, with a GL of 250. All food was prepared and provided by the Fred Hutch Human Nutrition Laboratory (HNL) during the intervention. Weekday dinners were consumed under supervision at the HNL, and the next day’s breakfast, lunch and snacks were portioned, packaged and taken home for consumption. Examples of study menus and detail on diet consumption have been published previously (Neuhouser et al. 2012).

Treatment ID:

TR001579

Treatment Summary:

A 7-day rotating menu was created for each diet. At baseline, participants completed a 3-d food record to estimate mean daily calorie intake. Energy intake from the food records along with weight, height, sex and activity level were used to estimate each participant’s daily energy needs necessary to maintain the current weight. The estimated calorie intake was used to adjust the 7-day rotating menu to meet each participant’s needs so that they would remain weight stable during the study. The percentage energy from macronutrients of the two diets were identical: 15% energy from protein, 30% energy from fat, and 55% energy from carbohydrate. The LGL diet provided on average 55 g/d of fiber and 77 g/d of fructose, with a GL of 125 (Table 1). The HGL diet substituted refined grains for whole grains, included other carbohydrates from high-glycemic index food sources and provided on average 28 g/d of fiber and 26 g/d of fructose, with a GL of 250. All food was prepared and provided by the Fred Hutch Human Nutrition Laboratory (HNL) during the intervention. Weekday dinners were consumed under supervision at the HNL, and the next day’s breakfast, lunch and snacks were portioned, packaged and taken home for consumption. Examples of study menus and detail on diet consumption have been published previously (Neuhouser et al. 2012).

Sample Preparation:

Sampleprep ID:	SP001572
Sampleprep Summary:	Lipidomics Sample Preparation and Mass Spectrometry Frozen plasma samples were thawed at room temperature (25 °C) for 30 min, vortexed, and 25 µL plasma was transferred to a borosilicate glass culture tube (16 x 100 mm). Next, 0.475 mL water, 1.45 mL 1:0.45 methanol:dichloromethane, and 25 µL isotope-labeled internal standards mixture were added to the tube. The Lipidyzer isotope labeled internal standards mixture consisted of 54 isotopes from 13 lipid classes (Sciex, Framingham, MA). The mixture was vortexed for 5 sec and incubated at room temperature for 30 min. Next, another 0.5 mL water and 0.45 mL dichloromethane were added to the tube, followed by gentle vortexing for 5 sec, and centrifugation at 2500 g at 15 °C for 10 min. The bottom organic layer was transferred to a new tube and 0.9 mL of dichloromethane was added to the original tube for a second extraction. The combined extracts were concentrated under nitrogen and reconstituted in 0.25 mL of the mobile phase (10 mM ammonium acetate in 50:50 methanol:dichloromethane). Quantitative lipidomics was performed with the Sciex Lipidyzer platform consisting of Shimadzu Nexera X2 LC-30AD pumps, a Shimadzu Nexera X2 SIL-30AC autosampler, and a Sciex QTRAP® 5500 mass spectrometer equipped with SelexION® for differential mobility spectrometry (DMS). 1-propanol was used as the chemical modifier for the DMS. Samples were introduced to the mass spectrometer by flow injection at 8 µL/min. Each sample was injected twice, once with the DMS on [phosphatidylcholines (PC); phosphatidylethanolamines (PE); lysophosphatidylcholines (LPC); lysophosphatidylethanolamines (LPE); sphingomyelins (SM)], and once with the DMS off ([cholesterol esters (CE); ceramides (CER); diacylglycerols (DAG); dihydroceramides (DCER)/ free fatty acids(FFA); hexosylceramides (HCER); lactosylceramides (LCER); triacylglycerols (TAG)]. The lipid molecular species were measured using multiple reaction monitoring and positive/negative polarity switching. Positive ion mode detected lipid classes SM, DAG, CE, CER, DCER, HCER, DCER, and TAG, and negative ion mode detected lipid classes LPE, LPC, PC, PE, and FFA. A total of 1070 lipids and fatty acids were targeted in the analysis. Data was acquired and processed using Analyst 1.6.3 and Lipidomics Workflow Manager 1.0.5.0.

Sampleprep ID:

SP001572

Sampleprep Summary:

Lipidomics Sample Preparation and Mass Spectrometry Frozen plasma samples were thawed at room temperature (25 °C) for 30 min, vortexed, and 25 µL plasma was transferred to a borosilicate glass culture tube (16 x 100 mm). Next, 0.475 mL water, 1.45 mL 1:0.45 methanol:dichloromethane, and 25 µL isotope-labeled internal standards mixture were added to the tube. The Lipidyzer isotope labeled internal standards mixture consisted of 54 isotopes from 13 lipid classes (Sciex, Framingham, MA). The mixture was vortexed for 5 sec and incubated at room temperature for 30 min. Next, another 0.5 mL water and 0.45 mL dichloromethane were added to the tube, followed by gentle vortexing for 5 sec, and centrifugation at 2500 g at 15 °C for 10 min. The bottom organic layer was transferred to a new tube and 0.9 mL of dichloromethane was added to the original tube for a second extraction. The combined extracts were concentrated under nitrogen and reconstituted in 0.25 mL of the mobile phase (10 mM ammonium acetate in 50:50 methanol:dichloromethane). Quantitative lipidomics was performed with the Sciex Lipidyzer platform consisting of Shimadzu Nexera X2 LC-30AD pumps, a Shimadzu Nexera X2 SIL-30AC autosampler, and a Sciex QTRAP® 5500 mass spectrometer equipped with SelexION® for differential mobility spectrometry (DMS). 1-propanol was used as the chemical modifier for the DMS. Samples were introduced to the mass spectrometer by flow injection at 8 µL/min. Each sample was injected twice, once with the DMS on [phosphatidylcholines (PC); phosphatidylethanolamines (PE); lysophosphatidylcholines (LPC); lysophosphatidylethanolamines (LPE); sphingomyelins (SM)], and once with the DMS off ([cholesterol esters (CE); ceramides (CER); diacylglycerols (DAG); dihydroceramides (DCER)/ free fatty acids(FFA); hexosylceramides (HCER); lactosylceramides (LCER); triacylglycerols (TAG)]. The lipid molecular species were measured using multiple reaction monitoring and positive/negative polarity switching. Positive ion mode detected lipid classes SM, DAG, CE, CER, DCER, HCER, DCER, and TAG, and negative ion mode detected lipid classes LPE, LPC, PC, PE, and FFA. A total of 1070 lipids and fatty acids were targeted in the analysis. Data was acquired and processed using Analyst 1.6.3 and Lipidomics Workflow Manager 1.0.5.0.

Combined analysis:

Analysis ID	AN002468	AN002469
Analysis type	MS	MS
Chromatography type	None (Direct infusion)	None (Direct infusion)
Chromatography system	Triple quadrupole	Triple quadrupole
Column	ESI	ESI
MS Type	ESI	ESI
MS instrument type	Triple quadrupole	Triple quadrupole
MS instrument name	ABI Sciex 5500 QTrap	ABI Sciex 5500 QTrap
Ion Mode	UNSPECIFIED	UNSPECIFIED
Units	mM	mM

Chromatography:

Chromatography ID:	CH001809
Chromatography Summary:	Quantitative lipidomics was performed with the Sciex Lipidyzer platform consisting of Shimadzu Nexera X2 LC-30AD pumps, a Shimadzu Nexera X2 SIL-30AC autosampler, and a Sciex QTRAP® 5500 mass spectrometer equipped with SelexION® for differential mobility spectrometry (DMS). 1-propanol was used as the chemical modifier for the DMS. Samples were introduced to the mass spectrometer by flow injection analysis at 8 uL/min aka direct infusion. Each sample was injected twice, once with the DMS on Method 1 (PC/PE/LPC/LPE/SM), and once with the DMS off Method 2 (CE/CER/DAG/DCER/FFA/HCER/LCER/TAG). The lipid molecular species were measured using multiple reaction monitoring (MRM) and positive/negative polarity switching. Positive ion mode detected lipid classes SM/DAG/CE/CER/DCER/HCER/LCER/TAG and negative ion mode detected lipid classes LPE/LPC/PC/PE/FFA. A total of 1070 lipids and fatty acids were targeted in the analysis.
Instrument Name:	Triple quadrupole
Column Name:	ESI
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS002288
Analysis ID:	AN002468
Instrument Name:	ABI Sciex 5500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Quantitative lipidomics was performed with the Sciex Lipidyzer platform consisting of Shimadzu Nexera X2 LC-30AD pumps, a Shimadzu Nexera X2 SIL-30AC autosampler, and a Sciex QTRAP® 5500 mass spectrometer equipped with SelexION® for differential mobility spectrometry (DMS). 1-propanol was used as the chemical modifier for the DMS. Samples were introduced to the mass spectrometer by flow injection analysis at 8 uL/min aka direct infusion. Each sample was injected twice, once with the DMS on Method 1 (PC/PE/LPC/LPE/SM)
Ion Mode:	UNSPECIFIED

MS ID:	MS002289
Analysis ID:	AN002469
Instrument Name:	ABI Sciex 5500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Quantitative lipidomics was performed with the Sciex Lipidyzer platform consisting of Shimadzu Nexera X2 LC-30AD pumps, a Shimadzu Nexera X2 SIL-30AC autosampler, and a Sciex QTRAP® 5500 mass spectrometer equipped with SelexION® for differential mobility spectrometry (DMS). 1-propanol was used as the chemical modifier for the DMS. Samples were introduced to the mass spectrometer by flow injection analysis at 8 uL/min aka direct infusion. Each sample was injected twice once with the DMS off Method 2 (CE/CER/DAG/DCER/FFA/HCER/LCER/TAG)
Ion Mode:	UNSPECIFIED