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MB Sample ID: SA092065
| Local Sample ID: | Healthy9 |
| 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 |
Select appropriate tab below to view additional metadata details:
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:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Healthy9 | SA092065 | FL013204 | control | Condition |
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 |
