Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA308937

Local Sample ID:	DS1-123-132
Subject ID:	SU002970
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

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Subject:

Subject ID:	SU002970
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
DS1-123-132	SA308937	FL037189	REND	TIMEPOINT

Collection:

Collection ID:	CO002963
Collection Summary:	lumbar puncture for serum and CSF collection (stored at -80°C)
Sample Type:	Serum

Treatment:

Treatment ID:	TR002979
Treatment Summary:	A total of 180 candidates volunteered between September 26, 2017, and January 13, 2020. The study was conducted in three centers. Two Italian centers, the ‘IRCCS Casa Sollievo della Sofferenza’ Research Hospital (Site 1) and the ‘Santa Maria di Terni’ Hospital (Site 2) recruited patients and performed the MRI examinations. The Multiple Sclerosis Centre of the Neurocentre of Southern Switzerland (Site 3) performed the magnetic resonance imaging (MRI) analysis. The ICVI of the ACT was performed at Site 2. Screening was done one month prior to enrolment in the study. The run-in period started after the screening examination (Run-in-START) and lasted three months (Run-in-END). After screening in the two recruiting centers (as above), n= 15 subjects with active and non-active SPMS suffering from progressive disability were found to be eligible, consented, and were assigned a unique identification number. Participants, nine females and six males, had a mean age of 50 years (range: 38–57), and were recruited in similar proportions by the two study sites. The mean EDSS was 7.6 (range 7–8), mean disease duration was 23 years (range 14–30), and mean time from diagnosis to secondary progression was 10 years (range: 1–20). The hNSC-SPMS study was advertised using the website of the hospitals and social media (eg Facebook and Twitter). The first patient selection was performed based on the documentation provided. Selected patients were then summoned in Site 1 and Site 2 (as above) for a first pre-screening meeting with the clinicians. Patients who agreed to participate were then subjected to the screening visit for the clinical trial. Following the surgical procedure, follow-up visits were performed monthly up to 12 months. Before transplantation, all patients underwent the following examinations (at both Run-in-START and Run-in-END): physical and neurological exams; vital signs; pregnancy tests (in fertile women); haematological and urine tests; lumbar puncture for serum and CSF collection (stored at -80°C);

Treatment ID:

TR002979

Treatment Summary:

A total of 180 candidates volunteered between September 26, 2017, and January 13, 2020. The study was conducted in three centers. Two Italian centers, the ‘IRCCS Casa Sollievo della Sofferenza’ Research Hospital (Site 1) and the ‘Santa Maria di Terni’ Hospital (Site 2) recruited patients and performed the MRI examinations. The Multiple Sclerosis Centre of the Neurocentre of Southern Switzerland (Site 3) performed the magnetic resonance imaging (MRI) analysis. The ICVI of the ACT was performed at Site 2. Screening was done one month prior to enrolment in the study. The run-in period started after the screening examination (Run-in-START) and lasted three months (Run-in-END). After screening in the two recruiting centers (as above), n= 15 subjects with active and non-active SPMS suffering from progressive disability were found to be eligible, consented, and were assigned a unique identification number. Participants, nine females and six males, had a mean age of 50 years (range: 38–57), and were recruited in similar proportions by the two study sites. The mean EDSS was 7.6 (range 7–8), mean disease duration was 23 years (range 14–30), and mean time from diagnosis to secondary progression was 10 years (range: 1–20). The hNSC-SPMS study was advertised using the website of the hospitals and social media (eg Facebook and Twitter). The first patient selection was performed based on the documentation provided. Selected patients were then summoned in Site 1 and Site 2 (as above) for a first pre-screening meeting with the clinicians. Patients who agreed to participate were then subjected to the screening visit for the clinical trial. Following the surgical procedure, follow-up visits were performed monthly up to 12 months. Before transplantation, all patients underwent the following examinations (at both Run-in-START and Run-in-END): physical and neurological exams; vital signs; pregnancy tests (in fertile women); haematological and urine tests; lumbar puncture for serum and CSF collection (stored at -80°C);

Sample Preparation:

Sampleprep ID:	SP002976
Sampleprep Summary:	Extraction of metabolites and lipids from serum and cerebrospinal fluid (CSF) was as follows: 40 µL CSF or serum was aliquoted into 2mL deep well plates followed by an addition of 360 µL cold MeOH:MeCN:H2O (5:3:2, v:v:v). Plates were then placed on a shaker at 4°C and plate shaker was set to 400 RPM for 30 minutes. Insoluble material was pelleted by centrifugation (4000 RPM, 10 min) and supernatants were isolated for analysis by UHPLC-MS. All 96-well plate pipetting was done using Integra MINI 96 (Integra Biosciences).

Sampleprep ID:

SP002976

Sampleprep Summary:

Extraction of metabolites and lipids from serum and cerebrospinal fluid (CSF) was as follows: 40 µL CSF or serum was aliquoted into 2mL deep well plates followed by an addition of 360 µL cold MeOH:MeCN:H2O (5:3:2, v:v:v). Plates were then placed on a shaker at 4°C and plate shaker was set to 400 RPM for 30 minutes. Insoluble material was pelleted by centrifugation (4000 RPM, 10 min) and supernatants were isolated for analysis by UHPLC-MS. All 96-well plate pipetting was done using Integra MINI 96 (Integra Biosciences).

Combined analysis:

Analysis ID	AN004684	AN004685	AN004686	AN004687	AN004688
Analysis type	MS	MS	MS	MS	MS
Chromatography type	Reversed phase	Reversed phase	Reversed phase	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish	Thermo Vanquish	Thermo Vanquish	Thermo Vanquish
Column	Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)	Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)	Phenomenex Kinetex C18 (30 x 2.1mm, 1.7um)	Phenomenex Kinetex C18 (30 x 2.1mm, 1.7um)	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
MS Type	ESI	ESI	ESI	ESI	EI
MS instrument type	Orbitrap	Orbitrap	Orbitrap	Orbitrap	Orbitrap
MS instrument name	Thermo Orbitrap Exploris 120	Thermo Orbitrap Exploris 120	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE	NEGATIVE
Units	Peak area	Peak area	Peak area	Peak area	Peak area

Chromatography:

Chromatography ID:	CH003526
Chromatography Summary:	Metabolomics Positive
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Column Temperature:	45
Flow Gradient:	0 min - 0.45 ml/min - 5% B, 0.5 min - 0.45ml/min - 5% B, 1.1 min - 0.45ml/min - 95% B, 2.75 min - 0.45ml/min - 95% B, 3 min - 0.45ml/min - 5% B, 5min - 0.45ml/min - 5%B
Flow Rate:	0.45 ml/min
Solvent A:	0.1% Formic Acid in Water
Solvent B:	0.1% Formic Acid in ACN
Chromatography Type:	Reversed phase

Chromatography ID:	CH003527
Chromatography Summary:	Metabolomics Negative
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Column Temperature:	45
Flow Gradient:	0 min - 0.45 ml/min - 0% B, 0.5 min - 0.45ml/min - 0% B, 1.1 min - 0.45ml/min - 100% B, 2.75 min - 0.45ml/min - 100% B, 3 min - 0.45ml/min - 0% B, 5min - 0.45ml/min - 0%B
Flow Rate:	0.45 ml/min
Solvent A:	5% ACN 95% Water 1mM Ammonium Acetate
Solvent B:	95% ACN 5% Water 1mM Ammonium Acetate
Chromatography Type:	Reversed phase

Chromatography ID:	CH003528
Chromatography Summary:	Lipidomics Positive
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (30 x 2.1mm, 1.7um)
Column Temperature:	50
Flow Gradient:	0 min - 0.3ml/min - 30%B, 3 min - 0.3ml/min - 100%B, 4.2min - 0.3ml/min - 100%B, 4.3min - 0.4ml/min - 30%B, 4.9min - 0/4ml/min - 30%B, 5 min - 0.3ml/min 30%B
Flow Rate:	0.3-0.4ml/min
Solvent A:	75:25 H2O:ACN 5mM NH4OAc
Solvent B:	90:10 iPrOH:ACN 5mM NH4OAc
Chromatography Type:	Reversed phase

Chromatography ID:	CH003529
Chromatography Summary:	Lipidomics Negative
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (30 x 2.1mm, 1.7um)
Column Temperature:	50
Flow Gradient:	0 min - 0.3ml/min - 10%B, 3 min - 0.3ml/min - 95%B, 4.2min - 0.3ml/min - 95%B, 4.3min - 0.45ml/min - 10%B, 4.9min - 0.4ml/min - 10%B, 5 min - 0.3ml/min 10%B
Flow Rate:	0.3-0.45ml/min
Solvent A:	75:25 H2O:ACN 5mM NH4OAc
Solvent B:	90:10 iPrOH:ACN 5mM NH4OAc
Chromatography Type:	Reversed phase

Chromatography ID:	CH003530
Chromatography Summary:	Oxylipin Negative
Instrument Name:	Thermo Vanquish
Column Name:	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:	60
Flow Gradient:	0min - 0.35ml/min - 0%B, 0.5min - 0.35ml/min - 25%B, 1min - 0.35ml/min - 25%B, 2.5min - 0.35ml/min - 40%B, 2.6min -0.35ml/min - 55%B, 4.5min - 0.35ml/min - 70%B, 4.6min - 0.35ml/min - 100%B, 6min - 0.35ml/min - 100%B, 6.1min - 0.35ml/min - 0%B, 7min - 0.35ml/min 0%B
Flow Rate:	0.35ml/min
Solvent A:	20:80:0.02 ACN:Water:Formic Acid
Solvent B:	20:80:0.02 ACN:IPA:Formic Acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004431
Analysis ID:	AN004684
Instrument Name:	Thermo Orbitrap Exploris 120
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Software for Feature Assignments - El-Maven
Ion Mode:	POSITIVE

MS ID:	MS004432
Analysis ID:	AN004685
Instrument Name:	Thermo Orbitrap Exploris 120
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Software for Feature Assignments - El-Maven
Ion Mode:	NEGATIVE

MS ID:	MS004433
Analysis ID:	AN004686
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Software for Feature Assignments - LipidSearch
Ion Mode:	POSITIVE

MS ID:	MS004434
Analysis ID:	AN004687
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Software for Feature Assignments - LipidSearch
Ion Mode:	NEGATIVE

MS ID:	MS004435
Analysis ID:	AN004688
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	EI
MS Comments:	Software for Feature Assignments - El-Maven
Ion Mode:	NEGATIVE