Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA125949

Local Sample ID:	SC_20191202_FMS_Embryo_S09_T2
Subject ID:	SU001568
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

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Subject:

Subject ID:	SU001568
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
SC_20191202_FMS_Embryo_S09_T2	SA125949	FL015464	No embryos_drops	Device

Collection:

Collection ID:	CO001563
Collection Summary:	Samples were collected from microdrops and microfluidic devices when embryos developed to fully expanded blastocyst stage, to allow stage-matched comparison of embryo metabolite production/consumption.
Sample Type:	Blastocysts

Treatment:

Treatment ID:	TR001583
Treatment Summary:	Control KSOM: fresh medium at day 0 not incubated in devices or microdrops. Day 4 KSOM_drop: medium incubated in microdrops for 4 days without embryos Day 5 KSOM_device: medium incubated in devices for 5 days without embryos Day 4 KSOM_drop_embryos: medium incubated in microdrops for 4 days with embryos Day 5 KSOM_device_embryos: medium incubated in devices for 5 days with embryos

Sample Preparation:

Sampleprep ID:	SP001576
Sampleprep Summary:	Culture media samples (100 µl) were thawed on ice and prepared using previously described methods. Briefly, 300 µL of dry ice cooled methanol was added to individual culture medium samples and incubated overnight at -80°C; individual samples were spun down to remove proteins and subsequent supernatant used for analyses. Samples were separated and analysed using reverse-phase liquid chromatography connected to a a Thermo Scientific Q Exactive HF (LC-Hybrid Quadrupole-Orbitrap MS/MS) instrument using positive ion mode MS.

Sampleprep ID:

SP001576

Sampleprep Summary:

Culture media samples (100 µl) were thawed on ice and prepared using previously described methods. Briefly, 300 µL of dry ice cooled methanol was added to individual culture medium samples and incubated overnight at -80°C; individual samples were spun down to remove proteins and subsequent supernatant used for analyses. Samples were separated and analysed using reverse-phase liquid chromatography connected to a a Thermo Scientific Q Exactive HF (LC-Hybrid Quadrupole-Orbitrap MS/MS) instrument using positive ion mode MS.

Combined analysis:

Analysis ID	AN002476	AN002477
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Thermo Hypersil Gold (100 x 2.1mm,1.9um)	Thermo Hypersil Gold (100 x 2.1mm,1.9um)
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	POSITIVE
Units	peak area	peak area

Chromatography:

Chromatography ID:	CH001814
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Hypersil Gold (100 x 2.1mm,1.9um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002296
Analysis ID:	AN002476
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Full MS analyses were acquired over a mass range of m/z 70-1050 under an ESI positive profile mode. Full mass scan was used at a resolution of 120,000 with a scan rate at ∼3.5 Hz Raw data were imported, processed, normalized, and reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK). All FMS sample runs were aligned against a FMS QC pool reference, with alignment to the reference being ≥ 96%, demonstrating the reproducibility of the RPLC column separation method. Peak picking, with a minimum threshold of 100,000 ion intensity, was performed for individual aligned runs based on an aggregate run (representative of all ion peaks detected in all samples).
Ion Mode:	POSITIVE

MS ID:	MS002297
Analysis ID:	AN002477
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Full MS analyses were acquired over a mass range of m/z 70-1050 under an ESI positive profile mode. Full mass scan was used at a resolution of 120,000 with a scan rate at ∼3.5 Hz Raw data were imported, processed, normalized, and reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK). All FMS sample runs were aligned against a FMS QC pool reference, with alignment to the reference being ≥ 96%, demonstrating the reproducibility of the RPLC column separation method. Peak picking, with a minimum threshold of 100,000 ion intensity, was performed for individual aligned runs based on an aggregate run (representative of all ion peaks detected in all samples).
Ion Mode:	POSITIVE