Summary of Study ST001267

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 PR000852. The data can be accessed directly via it's Project DOI: 10.21228/M8JT4N This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST001267
Study Title	Mass spectrometry-based lipidomics of oral squamous cell carcinoma tissue reveals aberrant cholesterol and glycerophospholipid metabolism
Study Type	Case study
Study Summary	Comparison between the lipid profile in oral squamous cell carcinoma of the tongue and healthy epithelial tissue from the contralateral side of the tongue of the same patient.
Institute	University of Helsinki
Department	Department of Otorhinolaryngology-Head and Neck Cancer
Last Name	Silén
First Name	Suvi
Address	Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, PO Box 263, FI-00029 HUS, Helsinki, Finland
Email	Suvi.silen@helsinki.fi
Phone	NA
Submit Date	2019-10-09
Num Groups	2
Total Subjects	10
Num Males	6
Num Females	4
Raw Data Available	Yes
Analysis Type Detail	MS(Dir. Inf.)
Release Date	2020-04-13
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000852
Project DOI:	doi: 10.21228/M8JT4N
Project Title:	Mass spectrometry-based lipidomics of oral squamous cell carcinoma tissue reveals aberrant cholesterol and glycerophospholipid metabolism
Project Type:	Case study
Project Summary:	Comparison between the lipid profile in oral squamous cell carcinoma of the tongue and healthy epithelial tissue from the contralateral side of the tongue
Institute:	University of Helsinki
Department:	Department of Otorhinolaryngology-Head and Neck Cancer
Last Name:	Silén
First Name:	Suvi
Address:	Haartmaninkatu 3, Helsinki, Uusimaa, 00018, Finland
Email:	Suvi.silen@helsinki.fi
Phone:	NA

Subject:

Subject ID:	SU001335
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Age Or Age Range:	24-78
Gender:	Male and female
Human Ethnicity:	caucasian
Human Inclusion Criteria:	tumour has not yet been treated with surgery, radiotherapy or chemotherapy; primary tumour
Human Exclusion Criteria:	concurrent other tumour

Factors:

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

mb_sample_id	local_sample_id	Condition
SA092065	Healthy9	control
SA092066	Healthy5	control
SA092067	Healthy10	control
SA092068	Healthy1	control
SA092069	Healthy2	control
SA092070	Healthy8	control
SA092071	Healthy3	control
SA092072	Healthy7	control
SA092073	Healthy4	control
SA092074	Healthy6	control
SA092055	OSCC7	OSCC
SA092056	OSCC1	OSCC
SA092057	OSCC8	OSCC
SA092058	OSCC9	OSCC
SA092059	OSCC10	OSCC
SA092060	OSCC5	OSCC
SA092061	OSCC6	OSCC
SA092062	OSCC2	OSCC
SA092063	OSCC4	OSCC
SA092064	OSCC3	OSCC

Showing results 1 to 20 of 20

Showing results 1 to 20 of 20

Collection:

Collection ID:	CO001329
Collection Summary:	Samples were collected in the operating theatre prior to the bulk tumour excision, and were washed in PBS before being snap-frozen using dry ice-ethanol slush. They were then stored at -72 Celsius
Sample Type:	Tongue tissue
Storage Conditions:	Described in summary
Collection Vials:	cryotube
Storage Vials:	cryotube

Treatment:

Treatment ID:	TR001350
Treatment Summary:	Not applicable

Sample Preparation:

Sampleprep ID:	SP001343
Sampleprep Summary:	Frozen samples were homogenised in LC-MS grade water (LicChrosolv®): they were placed in a homogenisation bead tube and homogenised for 6 runs at 45 seconds at 6.5 m/s with 5 minutes incubation on ice in-between runs, then diluted to a concentration of 5mg/ml before being stored at -72ºC until further MS processing. MS-based lipid analysis was performed by Lipotype GmbH (Dresden, Germany). Lipids were extracted using a two-step chloroform/methanol procedure (25). Samples were spiked with internal lipid standard mixture containing: cardiolipin 16:1/15:0/15:0/15:0 (CL), ceramide 18:1;2/17:0 (Cer), diacylglycerol 17:0/17:0 (DAG), hexosylceramide 18:1;2/12:0 (HexCer), lyso-phosphatidate 17:0 (LPA), lyso-phosphatidylcholine 12:0 (LPC), lyso-phosphatidylethanolamine 17:1 (LPE), lyso-phosphatidylglycerol 17:1 (LPG), lyso-phosphatidylinositol 17:1 (LPI), lyso-phosphatidylserine 17:1 (LPS), phosphatidate 17:0/17:0 (PA), phosphatidylcholine 17:0/17:0 (PC), phosphatidylethanolamine 17:0/17:0 (PE), phosphatidylglycerol 17:0/17:0 (PG), phosphatidylinositol 16:0/16:0 (PI), phosphatidylserine 17:0/17:0 (PS), cholesterol ester 20:0 (CE), sphingomyelin 18:1;2/12:0;0 (SM), triacylglycerol 17:0/17:0/17:0 (TAG) and cholesterol D6 (Chol). After extraction, the organic phase was transferred to an infusion plate and dried in a speed vacuum concentrator. The first-step dry extract was re-suspended in 7.5 mM ammonium acetate in chloroform/methanol/propanol (1:2:4, V:V) and the 2nd step dry extract resuspended in 33% ethanol solution of methylamine in chloroform/methanol (0.003:5:1; V:V). All liquid handling steps were performed using Hamilton Robotics STARlet robotic platform with the Anti Droplet Control feature for organic solvents pipetting.

Sampleprep ID:

SP001343

Sampleprep Summary:

Frozen samples were homogenised in LC-MS grade water (LicChrosolv®): they were placed in a homogenisation bead tube and homogenised for 6 runs at 45 seconds at 6.5 m/s with 5 minutes incubation on ice in-between runs, then diluted to a concentration of 5mg/ml before being stored at -72ºC until further MS processing. MS-based lipid analysis was performed by Lipotype GmbH (Dresden, Germany). Lipids were extracted using a two-step chloroform/methanol procedure (25). Samples were spiked with internal lipid standard mixture containing: cardiolipin 16:1/15:0/15:0/15:0 (CL), ceramide 18:1;2/17:0 (Cer), diacylglycerol 17:0/17:0 (DAG), hexosylceramide 18:1;2/12:0 (HexCer), lyso-phosphatidate 17:0 (LPA), lyso-phosphatidylcholine 12:0 (LPC), lyso-phosphatidylethanolamine 17:1 (LPE), lyso-phosphatidylglycerol 17:1 (LPG), lyso-phosphatidylinositol 17:1 (LPI), lyso-phosphatidylserine 17:1 (LPS), phosphatidate 17:0/17:0 (PA), phosphatidylcholine 17:0/17:0 (PC), phosphatidylethanolamine 17:0/17:0 (PE), phosphatidylglycerol 17:0/17:0 (PG), phosphatidylinositol 16:0/16:0 (PI), phosphatidylserine 17:0/17:0 (PS), cholesterol ester 20:0 (CE), sphingomyelin 18:1;2/12:0;0 (SM), triacylglycerol 17:0/17:0/17:0 (TAG) and cholesterol D6 (Chol). After extraction, the organic phase was transferred to an infusion plate and dried in a speed vacuum concentrator. The first-step dry extract was re-suspended in 7.5 mM ammonium acetate in chloroform/methanol/propanol (1:2:4, V:V) and the 2nd step dry extract resuspended in 33% ethanol solution of methylamine in chloroform/methanol (0.003:5:1; V:V). All liquid handling steps were performed using Hamilton Robotics STARlet robotic platform with the Anti Droplet Control feature for organic solvents pipetting.

Combined analysis:

Analysis ID	AN002104
Analysis type	MS
Chromatography type	None (Direct infusion)
Chromatography system	none
Column	none
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap
Ion Mode	UNSPECIFIED
Units	pmol

Chromatography:

Chromatography ID:	CH001536
Instrument Name:	none
Column Name:	none
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS001955
Analysis ID:	AN002104
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	POSITIVE AND NEGATIVE MODES IN ESI. MS AND MS2 MODES WERE USED. Different sample amounts were injected into the MS (described in the metadata), so before data analysis, the raw abundances in pmol need to be normalised to the amount injected. The raw data provided is in pmol per amount injected into the MS. As different amounts were injected you need to divide by the amount injected and the original concentration of the sample (which was 5mg/ml) to get pmol/mg of tissue weight. The detection limit given by Lipotype Ltd for the machine is 1pmol, and values less than that should also be removed from the raw data before analysis. When we normalised the data (normalised data not provided here), we required the presence of 80% or more 'non-zero' values in either group. Otherwise the feature was excluded.
Ion Mode:	UNSPECIFIED