Summary of Study ST001440

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 PR000990. The data can be accessed directly via it's Project DOI: 10.21228/M8QQ45 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.

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Study ID	ST001440
Study Title	Developing preliminary blood metabolomics-based biomarkers of insufficient sleep in humans
Study Summary	Study Objective: Identify small molecule biomarkers of insufficient sleep using untargeted plasma metabolomics in humans undergoing experimental insufficient sleep. Methods: We conducted a cross-over laboratory study where 16 normal weight participants (8 men; age 22 ± 5 years; body mass index < 25 kg/m2) completed three baseline days (BL; 9h sleep opportunity per night) followed by five day insufficient (5H; 5h sleep opportunity per night) and adequate (9H; 9h sleep opportunity per night) sleep conditions. Energy balanced diets were provided during baseline, with ad libitum energy intake provided during the insufficient and adequate sleep conditions. Untargeted plasma metabolomics analyses were performed using blood samples collected every 4h across the final 24h of each condition. Biomarker models were developed using logistic regression and linear support vector machine algorithms. Results: The top performing biomarker model was developed by linear support vector machine modeling, consisted of 65 compounds, and discriminated insufficient versus adequate sleep with 74% overall accuracy and a Matthew’s Correlation Coefficient of 0.39. The compounds in the top performing biomarker model were associated with ATP Binding Cassette Transporters in Lipid Homeostasis, Phospholipid Metabolic Process, Plasma Lipoprotein Remodeling, and sphingolipid metabolism. Conclusion: We identified potential metabolomics-based biomarkers of insufficient sleep in humans. Further development and validation of omics-based biomarkers of insufficient sleep will advance our understanding of the negative consequences of insufficient sleep, improve diagnosis of poor sleep health, and identify targets for countermeasures designed to mitigate the negative health consequences of insufficient sleep.
Institute	University of Colorado Boulder
Last Name	Depner
First Name	Christopher
Address	354 UCB, Clare Small Room 114
Email	christopher.depner@colorado.edu
Phone	5098799151
Submit Date	2019-08-29
Raw Data Available	Yes
Analysis Type Detail	LC-MS
Release Date	2021-08-09
Release Version	1

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Project:

Project ID:	PR000990
Project DOI:	doi: 10.21228/M8QQ45
Project Title:	Developing preliminary blood metabolomics-based biomarkers of insufficient sleep in humans
Project Type:	Human clinical translational study
Project Summary:	Study Objective: Identify small molecule biomarkers of insufficient sleep using untargeted plasma metabolomics in humans undergoing experimental insufficient sleep. Methods: We conducted a cross-over laboratory study where 16 normal weight participants (8 men; age 22 ± 5 years; body mass index < 25 kg/m2) completed three baseline days (BL; 9h sleep opportunity per night) followed by five day insufficient (5H; 5h sleep opportunity per night) and adequate (9H; 9h sleep opportunity per night) sleep conditions. Energy balanced diets were provided during baseline, with ad libitum energy intake provided during the insufficient and adequate sleep conditions. Untargeted plasma metabolomics analyses were performed using blood samples collected every 4h across the final 24h of each condition. Biomarker models were developed using logistic regression and linear support vector machine algorithms. Results: The top performing biomarker model was developed by linear support vector machine modeling, consisted of 65 compounds, and discriminated insufficient versus adequate sleep with 74% overall accuracy and a Matthew’s Correlation Coefficient of 0.39. The compounds in the top performing biomarker model were associated with ATP Binding Cassette Transporters in Lipid Homeostasis, Phospholipid Metabolic Process, Plasma Lipoprotein Remodeling, and sphingolipid metabolism. Conclusion: We identified potential metabolomics-based biomarkers of insufficient sleep in humans. Further development and validation of omics-based biomarkers of insufficient sleep will advance our understanding of the negative consequences of insufficient sleep, improve diagnosis of poor sleep health, and identify targets for countermeasures designed to mitigate the negative health consequences of insufficient sleep.
Institute:	University of Colorado Boulder
Department:	Integrative Physiology
Laboratory:	Sleep and Chronobiology Laboratory, University of Colorado Boulder
Last Name:	Depner
First Name:	Christopher
Address:	354 UCB
Email:	christopher.depner@colorado.edu
Phone:	5098799151
Funding Source:	NIH; Sleep Research Society Foundation

Subject:

Subject ID:	SU001514
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Gender	Time	Sleep Window (Hours)
SA122110	12_5H_12	F	12	5H
SA122111	10_5H_12	F	12	5H
SA122112	17_5H_12	F	12	5H
SA122113	7_5H_12	F	12	5H
SA122114	510_5H_12	F	12	5H
SA122115	3_5H_12	F	12	5H
SA122116	15_5H_12	F	12	5H
SA122117	7_9H_12	F	12	9H
SA122118	15_9H_12	F	12	9H
SA122119	13_9H_12	F	12	9H
SA122120	10_9H_12	F	12	9H
SA122121	17_9H_12	F	12	9H
SA122122	12_9H_12	F	12	9H
SA122123	510_9H_12	F	12	9H
SA122124	3_9H_12	F	12	9H
SA122125	3_BL_12	F	12	BL
SA122126	15_BL_12	F	12	BL
SA122127	13_BL_12	F	12	BL
SA122128	17_BL_12	F	12	BL
SA122129	12_BL_12	F	12	BL
SA122130	10_BL_12	F	12	BL
SA122131	10_5H_16	F	16	5H
SA122132	7_5H_16	F	16	5H
SA122133	17_5H_16	F	16	5H
SA122134	15_5H_16	F	16	5H
SA122135	3_5H_16	F	16	5H
SA122136	12_5H_16	F	16	5H
SA122137	510_5H_16	F	16	5H
SA122138	7_9H_16	F	16	9H
SA122139	510_9H_16	F	16	9H
SA122140	15_9H_16	F	16	9H
SA122141	3_9H_16	F	16	9H
SA122142	10_9H_16	F	16	9H
SA122143	17_9H_16	F	16	9H
SA122144	17_BL_16	F	16	BL
SA122145	3_BL_16	F	16	BL
SA122146	10_BL_16	F	16	BL
SA122147	12_BL_16	F	16	BL
SA122148	15_BL_16	F	16	BL
SA122149	7_5H_20	F	20	5H
SA122150	12_5H_20	F	20	5H
SA122151	15_5H_20	F	20	5H
SA122152	17_5H_20	F	20	5H
SA122153	3_5H_20	F	20	5H
SA122154	15_9H_20	F	20	9H
SA122155	17_9H_20	F	20	9H
SA122156	10_9H_20	F	20	9H
SA122157	12_9H_20	F	20	9H
SA122158	13_9H_20	F	20	9H
SA122159	3_9H_20	F	20	9H
SA122160	7_9H_20	F	20	9H
SA122161	10_BL_20	F	20	BL
SA122162	12_BL_20	F	20	BL
SA122163	3_BL_20	F	20	BL
SA122164	15_BL_20	F	20	BL
SA122165	17_BL_20	F	20	BL
SA122166	15_5H_4	F	4	5H
SA122167	10_5H_4	F	4	5H
SA122168	510_5H_4	F	4	5H
SA122169	12_5H_4	F	4	5H
SA122170	3_5H_4	F	4	5H
SA122171	7_5H_4	F	4	5H
SA122172	17_5H_4	F	4	5H
SA122173	3_9H_4	F	4	9H
SA122174	510_9H_4	F	4	9H
SA122175	13_9H_4	F	4	9H
SA122176	7_9H_4	F	4	9H
SA122177	15_9H_4	F	4	9H
SA122178	10_9H_4	F	4	9H
SA122179	12_9H_4	F	4	9H
SA122180	17_9H_4	F	4	9H
SA122181	12_BL_4	F	4	BL
SA122182	3_BL_4	F	4	BL
SA122183	15_BL_4	F	4	BL
SA122184	13_BL_4	F	4	BL
SA122185	17_BL_4	F	4	BL
SA122186	10_BL_4	F	4	BL
SA122187	12_5H_8	F	8	5H
SA122188	10_5H_8	F	8	5H
SA122189	510_5H_8	F	8	5H
SA122190	3_5H_8	F	8	5H
SA122191	15_5H_8	F	8	5H
SA122192	17_5H_8	F	8	5H
SA122193	7_5H_8	F	8	5H
SA122194	3_9H_8	F	8	9H
SA122195	12_9H_8	F	8	9H
SA122196	10_9H_8	F	8	9H
SA122197	7_9H_8	F	8	9H
SA122198	15_9H_8	F	8	9H
SA122199	510_9H_8	F	8	9H
SA122200	17_9H_8	F	8	9H
SA122201	13_9H_8	F	8	9H
SA122202	12_BL_8	F	8	BL
SA122203	3_BL_8	F	8	BL
SA122204	15_BL_8	F	8	BL
SA122205	10_BL_8	F	8	BL
SA122206	17_BL_8	F	8	BL
SA122207	17_5H_0	F	zero	5H
SA122208	12_5H_0	F	zero	5H
SA122209	15_5H_0	F	zero	5H

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Collection:

Collection ID:	CO001509
Collection Summary:	These blood (plasma) samples were collected through an IV catheter in human participants in a Clinical Translational Study investigating the metabolic consequences of insufficient sleep.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR001529
Treatment Summary:	This was a cross-over design with baseline (BL; 9h per night sleep with controlled energy intake), control (9H; 9h per night sleep with ad libitum energy intake), and insufficient sleep (5H; 5h per night sleep with ad libitum energy intake) conditions. Baseline lasted 3 days and control and insufficient sleep conditions lasted 5 days.

Sample Preparation:

Sampleprep ID:	SP001522
Sampleprep Summary:	For sample preparation, plasma samples were thawed at room temperature and briefly vortexed. 100 uL of each sample was transferred to a 1.5 mL microcentrifuge tube and kept at 0°C. 10 uL of hydrophobic and hydrophilic standards and spikes at room temperature were added to each sample, and then each sample vortexed for 10s. 400 uL of ice-cold methanol was added to precipitate proteins. Tubes were then vortexed for 10s and then centrifuged for 15 min at 0°C at 18,000 x g. The supernatant was transferred to a clean glass culture tube using a plastic pipette. Samples were dried in glass culture tubes placed under N2 at 35°C for approximately 1h. Using a glass pipette, 3 mL of methyl tert-butyl ether (MTBE) was added to the dried methanol residue in each glass culture tube. Tubes were vortexed for 30s. 750 uL of water was added and tubes were vortexed for 10s. Tubes were centrifuged for 10 min at room temperature at ~200 x g. 2.5 mL of the resulting MTBE layer (hydrophobic fraction) was transferred to a new glass culture tube; the remaining layer was the hydrophilic fraction. 3.0 mL of MTBE was added to the remaining hydrophilic fraction and tubes were vortexed for 10s. These tubes were again centrifuged for 10 min at room temperature at ~200 x g. 3.0 mL of MTBE was aspirated and combined with the first MTBE layer. The MTBE fractions were dried under N2 at 35°C and immediately re-suspended in 200 uL of methanol. Each tube was vortexed for 5s, transferred to a glass auto-sampler vial with a glass insert using a Pasteur pipette. Samples were stored at -80°C. The hydrophilic fractions were dried under N2 at 35°C. 100 uL of water and 400 uL of ice-cold methanol were added to the dried hydrophilic fraction. Tubes were vortexed for 10s and centrifuged immediately at ~200 x g for 1 min. Supernatants from each tube were transferred to a 1.5 mL microcentrifuge tube using a Pasteur pipette. These tubes were then stored at -80°C for 25 min then centrifuged for 15 min at 0°C and 18,000 x g. The supernatant was transferred to a new 1.5 mL microcentrifuge tube using a plastic pipette. These tubes were dried in a vacuum centrifugal concentrator at 45°C and re-suspended in 100 uL of 95:5 water: acetonitrile. Each tube was vortexed for 30s and transferred to a glass auto-sampler vial with a glass insert using a plastic pipette tip. Samples were stored at -80°C.

Sampleprep ID:

SP001522

Sampleprep Summary:

For sample preparation, plasma samples were thawed at room temperature and briefly vortexed. 100 uL of each sample was transferred to a 1.5 mL microcentrifuge tube and kept at 0°C. 10 uL of hydrophobic and hydrophilic standards and spikes at room temperature were added to each sample, and then each sample vortexed for 10s. 400 uL of ice-cold methanol was added to precipitate proteins. Tubes were then vortexed for 10s and then centrifuged for 15 min at 0°C at 18,000 x g. The supernatant was transferred to a clean glass culture tube using a plastic pipette. Samples were dried in glass culture tubes placed under N2 at 35°C for approximately 1h. Using a glass pipette, 3 mL of methyl tert-butyl ether (MTBE) was added to the dried methanol residue in each glass culture tube. Tubes were vortexed for 30s. 750 uL of water was added and tubes were vortexed for 10s. Tubes were centrifuged for 10 min at room temperature at ~200 x g. 2.5 mL of the resulting MTBE layer (hydrophobic fraction) was transferred to a new glass culture tube; the remaining layer was the hydrophilic fraction. 3.0 mL of MTBE was added to the remaining hydrophilic fraction and tubes were vortexed for 10s. These tubes were again centrifuged for 10 min at room temperature at ~200 x g. 3.0 mL of MTBE was aspirated and combined with the first MTBE layer. The MTBE fractions were dried under N2 at 35°C and immediately re-suspended in 200 uL of methanol. Each tube was vortexed for 5s, transferred to a glass auto-sampler vial with a glass insert using a Pasteur pipette. Samples were stored at -80°C. The hydrophilic fractions were dried under N2 at 35°C. 100 uL of water and 400 uL of ice-cold methanol were added to the dried hydrophilic fraction. Tubes were vortexed for 10s and centrifuged immediately at ~200 x g for 1 min. Supernatants from each tube were transferred to a 1.5 mL microcentrifuge tube using a Pasteur pipette. These tubes were then stored at -80°C for 25 min then centrifuged for 15 min at 0°C and 18,000 x g. The supernatant was transferred to a new 1.5 mL microcentrifuge tube using a plastic pipette. These tubes were dried in a vacuum centrifugal concentrator at 45°C and re-suspended in 100 uL of 95:5 water: acetonitrile. Each tube was vortexed for 30s and transferred to a glass auto-sampler vial with a glass insert using a plastic pipette tip. Samples were stored at -80°C.

Combined analysis:

Analysis ID	AN002405	AN002406
Analysis type	MS	MS
Chromatography type	Reversed phase	HILIC
Chromatography system	Agilent 1290	Agilent 1200
Column	Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um)	Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Agilent 6220 TOF	Agilent 6520 QTOF
Ion Mode	POSITIVE	POSITIVE
Units	raw counts	raw counts

Chromatography:

Chromatography ID:	CH001767
Instrument Name:	Agilent 1290
Column Name:	Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um)
Chromatography Type:	Reversed phase

Chromatography ID:	CH001768
Instrument Name:	Agilent 1200
Column Name:	Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
Chromatography Type:	HILIC

MS:

MS ID:	MS002246
Analysis ID:	AN002405
Instrument Name:	Agilent 6220 TOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The hydrophobic fraction MS conditions were as follows: Agilent 6220 Time-of-Flight (TOF)-MS with dual ESI source, scan rate 2.02 spectra/s, mass range 60–1600 m/z, gas temperature 300°C, gas flow 12.0 L/min, nebulizer 30 psi, skimmer 60V, capillary voltage 4000V, fragmentor 120V, reference masses 121.050873 and 922.009798 (Agilent reference mix).
Ion Mode:	POSITIVE

MS ID:	MS002247
Analysis ID:	AN002406
Instrument Name:	Agilent 6520 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The hydrophilic fraction mass spectrometry conditions were as follows: Agilent 6520 Quadrupole Time-of-Flight mass spectrometer (Q-TOF-MS) in positive ionization mode with ESI source, mass range 50–1700 m/z, scan rate 2.21, gas temperature 300°C, gas flow 10.0L/min, nebulizer 30 psi, skimmer 60V, capillary voltage 4000V, fragmentor 120V, reference masses 121.050873 and 922.009798 (Agilent reference mix).
Ion Mode:	POSITIVE