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MB Sample ID: SA176616
| Local Sample ID: | C26 |
| Subject ID: | SU001983 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001983 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| C26 | SA176616 | FL021898 | Control | Diagnosis |
Collection:
| Collection ID: | CO001976 |
| Collection Summary: | Four calibrated and licensed dentists performed oral examinations, and saliva collection the same day as blood collection. All subjects were asked to refrain from eating, drinking, or brushing for at least 1 h prior to undergoing these procedures. The subject was asked to expectorate unstimulated whole saliva over a 10-min period into a 50-mL tube (Corning, Corning, NY, USA) kept on ice. Following incubation on ice for 15 min, the aqueous layer of each sample was pipetted off, and samples with volumes of at least 1 and 0.1 mL were aliquoted into 2-mL tubes kept at 4℃ in a CubeCooler® as study and quality control (QC) samples, respectively. Subsequently, they were frozen with liquid nitrogen and stored at −80℃ until analysis. |
| Sample Type: | Saliva |
Treatment:
| Treatment ID: | TR001995 |
| Treatment Summary: | Systemically healthy controls and T2D patients were recruited. |
Sample Preparation:
| Sampleprep ID: | SP001989 |
| Sampleprep Summary: | Saliva samples were thawed at 4℃, then vortexed and centrifuged (4 ℃, 18,000 × g) for 3 min. Next, 0.8 mL of the aqueous layer was pipetted off and weighed, then 0.3 mL of that was transferred into a 2-mL glass vial (Nichiden-Rika Glass, Kobe, Japan) and kept at 4℃ in a CubeCooler®. For extraction, 0.3 mL of deaerated MilliQ water containing ribitol (0.02 mg/mL) as an internal standard was added. After incubation using an Eppendorf thermomixer (25℃, 1000 rpm, 10 min), 1.4 mL of deaerated acetonitrile was added. After incubation (25℃, 1000 rpm, 10 min) and centrifugation (4℃, 1800 × g) for 3 min, 1.6 mL of the supernatant was transferred to a 2-mL tube and dried with a vacuum concentrator (VC-96R; TAITEC, Koshigaya, Japan) for 30 min, then allowed to lyophilize overnight. Derivatization was performed with a methoxyamine hydrochloride solution with pyridine at a concentration of 20 mg/mL, followed by silylation application of N-methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA). |
Combined analysis:
| Analysis ID | AN003102 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | GC-MS/MS-TQ8040 |
| Column | InertCap 5MS/NP capillary |
| MS Type | EI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Shimazu TQ8040 |
| Ion Mode | POSITIVE |
| Units | Intensity |
Chromatography:
| Chromatography ID: | CH002289 |
| Instrument Name: | GC-MS/MS-TQ8040 |
| Column Name: | InertCap 5MS/NP capillary |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002884 |
| Analysis ID: | AN003102 |
| Instrument Name: | Shimazu TQ8040 |
| Instrument Type: | Triple quadrupole |
| MS Type: | EI |
| MS Comments: | GC-MS data were converted into ABF format using an ABF converter, then processed using MS-DIAL (version 3.90) to perform feature detection, spectra deconvolution, metabolite identification, and peak alignment (Tsugawa et al. 2015). Normalization was then performed based on the internal standard (ribitol) as well as the LOWESS algorithm, whereby metabolic feature signal drift with time was independently corrected by fitting a LOWESS curve to the MS signal measured in QCs. |
| Ion Mode: | POSITIVE |
