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.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST001267
Study TitleMass spectrometry-based lipidomics of oral squamous cell carcinoma tissue reveals aberrant cholesterol and glycerophospholipid metabolism
Study TypeCase study
Study SummaryComparison 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
DepartmentDepartment of Otorhinolaryngology-Head and Neck Cancer
Last NameSilén
First NameSuvi
AddressDepartment of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, PO Box 263, FI-00029 HUS, Helsinki, Finland
EmailSuvi.silen@helsinki.fi
PhoneNA
Submit Date2019-10-09
Num Groups2
Total Subjects10
Num Males6
Num Females4
Raw Data AvailableYes
Analysis Type DetailLC-MS
Release Date2020-04-13
Release Version1
Suvi Silén Suvi Silén
https://dx.doi.org/10.21228/M8JT4N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA092065Healthy9control
SA092066Healthy5control
SA092067Healthy10control
SA092068Healthy1control
SA092069Healthy2control
SA092070Healthy8control
SA092071Healthy3control
SA092072Healthy7control
SA092073Healthy4control
SA092074Healthy6control
SA092055OSCC7OSCC
SA092056OSCC1OSCC
SA092057OSCC8OSCC
SA092058OSCC9OSCC
SA092059OSCC10OSCC
SA092060OSCC5OSCC
SA092061OSCC6OSCC
SA092062OSCC2OSCC
SA092063OSCC4OSCC
SA092064OSCC3OSCC
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.

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
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