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 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 DetailMS(Dir. Inf.)
Release Date2020-04-13
Release Version1
Suvi Silén Suvi Silén
https://dx.doi.org/10.21228/M8JT4N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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

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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