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MB Sample ID: SA025672
Local Sample ID: | Sa_pro_26 |
Subject ID: | SU000517 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Species Group: | Human |
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Subject:
Subject ID: | SU000517 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Species Group: | Human |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
Sa_pro_26 | SA025672 | FL006059 | Yes | debridement |
Collection:
Collection ID: | CO000511 |
Collection Summary: | The subjects were asked to refrain from brushing and using mouthwash for at least 1 hour prior to sample collection and periodontal examinations. We collected a minimum of 3 mL of unstimulated whole saliva between 1:00 and 3:00 p.m. Thereafter, saliva was sampled again at 15 minutes following removal of supragingival plaque and calculus with an ultrasonic scaler (debridement). Finally, 1 ml of each sample was immediately frozen with liquid nitrogen and stored at -80°C until analysis. |
Sample Type: | Saliva |
Treatment:
Treatment ID: | TR000531 |
Treatment Summary: | Debridement was performed with an ultrasonic scaler, as described in “Collection Summary”. To maintain the subgingival microbiota and avoid bleeding, we avoided insertion of the scalar tip into the gingival sulcus. |
Sample Preparation:
Sampleprep ID: | SP000524 |
Sampleprep Summary: | Frozen saliva samples were freeze-dried overnight using a freeze-dryer (VD-800F; TAITEC, Saitama, Japan), and metabolites were extracted with 1 ml of MeOH/H2O/CHCl3 (5/2/2, v/v/v). As an internal standard, 60 µl of ribitol (0.2 mg/ml) was added to the mixture. The sample was centrifuged at 16,000 g for 3 min at 4 °C, and the supernatant (900 µl) was transferred to another microtube and mixed with 400µl of water. After centrifugation at 16,000 g for 3 min at 4 °C, 800µl of the supernatant was transferred to another microtube whose cap was pierced. The extract was evaporated using a vacuum centrifuge dryer for 2 h in order to remove methanol, then freeze-dried overnight. For derivatization, 100 µl of methoxyamine hydrochloride (20 mg/ml in pyrimidine) and 50 µl of N-methyl-N-(trimethylsilyl)trifluoroacetamide were employed. The sample was then used for GCMS analysis, and a 1 µL of sample was injected in split mode (25/1, v/v). |
Combined analysis:
Analysis ID | AN000762 |
---|---|
Analysis type | MS |
Chromatography type | GC |
Chromatography system | Shimadzu GCMS-QP2010 ultra |
Column | a 30 m × 0.25 mm i.d. fused silica capillary column coated with 0.25 µm CP-SIL 8 CB low bleed (Varian Inc., Palo Alto, CA) |
MS Type | EI |
MS instrument type | GC-TOF |
MS instrument name | Shimadzu QP2010 Ultra |
Ion Mode | POSITIVE |
Units | Peak area |
Chromatography:
Chromatography ID: | CH000548 |
Chromatography Summary: | The device used was GCMS-QP2010 ultra (Shimadzu Inc., Kyoto, Japan) equipped with a 30 m × 0.25 mm i.d. fused silica capillary column coated with 0.25 µm CP-SIL 8 CB low bleed (Varian Inc., Palo Alto, CA) and AOC-20i (Shimadzu) as an autosampler. The injection temperature was 230 °C. The helium gas flow rate through the column was 1.12 ml/min. The column temperature was held at 80 °C for 2 min and then raised by 15 °C /min to 330 °C and held for 6 min. The transfer line and the ion source temperatures were 250 °C and 200 °C, respectively. Ions were generated by a 70 kV electron impact (EI), and 20 scans/sec were recorded over the mass range 85-500. A standard alkane mixture (C8-C40) was injected at the beginning of the analysis for subsequent identification of metabolites. |
Instrument Name: | Shimadzu GCMS-QP2010 ultra |
Column Name: | a 30 m × 0.25 mm i.d. fused silica capillary column coated with 0.25 µm CP-SIL 8 CB low bleed (Varian Inc., Palo Alto, CA) |
Column Temperature: | The column temperature was held at 80 °C for 2 min and then raised by 15 °C /min to 330 °C and held for 6 min. |
Flow Rate: | The helium gas flow rate through the column was 1.12 ml/min. |
Sample Injection: | 1 µL |
Chromatography Type: | GC |
MS:
MS ID: | MS000674 |
Analysis ID: | AN000762 |
Instrument Name: | Shimadzu QP2010 Ultra |
Instrument Type: | GC-TOF |
MS Type: | EI |
Ion Mode: | POSITIVE |