Return to study ST002328 main page
MB Sample ID: SA229535
| Local Sample ID: | B3p |
| Subject ID: | SU002415 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | N/A |
| Age Or Age Range: | 19-75 |
| Weight Or Weight Range: | N/A |
| Height Or Height Range: | N/A |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002415 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | N/A |
| Age Or Age Range: | 19-75 |
| Weight Or Weight Range: | N/A |
| Height Or Height Range: | N/A |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| B3p | SA229535 | FL028995 | PLWH | Treatment |
Collection:
| Collection ID: | CO002408 |
| Collection Summary: | Samples were collected in 50 mL sterile centrifuge tubes and immediately stored at −80°C. 100 μl frozen aliquots of human saliva samples were processed for metabolite extraction liquid chromatography-mass spectrometry (LC-MS) analysis commercially by Creative Proteomics. |
| Collection Protocol Filename: | Collection_protocol.pdf |
| Sample Type: | Saliva |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002427 |
| Treatment Summary: | Samples were collected from both the healthy subjects (Control) and subjects living with HIV+ under anti-retroviral therapy (PLWH) in 50 ml sterile centrifuge tubes and immediately stored at −80°C. 100 μl frozen aliquots of human saliva samples were processed for metabolite extraction liquid chromatography-mass spectrometry (LC-MS) analysis commercially by Creative Proteomics. |
| Treatment Protocol Filename: | Treatment_protocol.pdf |
Sample Preparation:
| Sampleprep ID: | SP002421 |
| Sampleprep Summary: | 100 μl of saliva samples were thawed, transferred to new tubes, extracted with 200 μl of 80% methanol, and vortexed for 30 seconds. Then the samples were kept at -40 °C for 1 hour, vortexed for 30 s, and centrifuged at 12000 rpm, 4 °C for 15 minutes. Finally, 200 μl of supernatant and 5 μl of DL-o-Chlorophenylalanine (1 mg/ml) were transferred to the vial for LC-MS analysis. Quality control (QC) samples were used to evaluate the methodology. The same amount of extract was obtained from each sample and mixed with QC samples. The QC sample was prepared using the same sample preparation procedure. Instrumental setup Separation was performed by Ultimate 3000LC combined with Q Exactive MS (Thermo) and screened with ESI-MS (targeted MS/MS mode). The LC system is comprised of an ACQUITY UPLC HSS T3 (100 × 2.1mm 1.8 μm) with Ultimate 3000LC. The mobile phase was composed of solvent A (0.05% formic acid-water) and solvent B (acetonitrile) with a gradient elution (0-1.0 min, 95% A; 1.0-12.0 min,95%-5% A; 12.0-13.5 min,5% A; 13.5-13.6 min, 5%-95% A; 13.6-16 min, 95% A). The flow rate of the mobile phase was 0.3 ml/min. The column temperature was maintained at 40 °C, and the sample manager temperature is set at 4 °C. Mass spectrometry parameters in ESI+ and ESI- mode are listed as follows: ESI+: Heater Temp 300 °C; Sheath Gas Flow rate, 45 arb; Aux Gas Flow Rate, 15 arb; Sweep Gas Flow Rate, 1 arb; spray voltage, 3.0 kV; Capillary Temp, 350 °C; S-Lens RF Level, 30%. ESI-: Heater Temp 300 °C, Sheath Gas Flow rate, 45 arb; Aux Gas Flow Rate, 15arb; Sweep Gas Flow Rate, 1 arb; spray voltage, 3.2 kV; Capillary Temp,350 °C; S-Lens RF Level, 60%. Bioinformatic data analysis included multivariate statistical analysis, single variable analysis, cluster analysis, and correlation network of differential metabolites. Statistically significant metabolites (FC >1.5) were integrated with differentially expressed genes obtained from the RNAseq data and the combined data was visualized with Metaboanalyst (https://www.metaboanalyst.ca/) and Cytoscape v3.8 via Metscape v3.1 plugin (https://cytoscape.org/). |
| Sampleprep Protocol Filename: | Sample_preparation.pdf |
| Processing Storage Conditions: | Described in summary |
| Extract Storage: | Described in summary |
Combined analysis:
| Analysis ID | AN003797 | AN003798 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | area | area |
Chromatography:
| Chromatography ID: | CH002810 |
| Methods Filename: | Chromatography_meta_data_queriesCP.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | (0-1.0 min, 95% A; 1.0-12.0 min,95%-5% A; 12.0-13.5 min,5% A; 13.5-13.6 min, 5%- 629 95% A; 13.6-16 min, 95% A |
| Flow Rate: | .3 ml/min |
| Injection Temperature: | 4 |
| Solvent A: | 100% water; 0.05% formic acid |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003539 |
| Analysis ID: | AN003797 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolomics was performed by Creative Proteomics. Gingival cells enriched in immune cells were prepared by removing epithelial cells based on gradient centrifugation. HOIL samples from three control individuals were pooled and compared with three independent HIV+ individuals. Separation was performed by Ultimate 3000LC combined with Q Exactive MS (Thermo) and screened with ESI-MS (targeted MS/MS mode). The software we used for metabolites identification is Compound Discoverer 3.1 SP1. For metabolites identification, the raw data are acquired and aligned using the Compound Discover based on the m/z value and the retention time of the ion signals. CD software offers a fully integrated suite of advanced software tools for known-parent and unknown data processing and interpretation. It is used for the initial metabolites identification. We also use mzMine2 software (with parameters of m/z tolerance=0.1 m/z ) for the online database search based on the MS1 and MS2 spectra acquired. The database used is HMDB. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MS_Metadata.docx |
| MS ID: | MS003540 |
| Analysis ID: | AN003798 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolomics was performed by Creative Proteomics. Gingival cells enriched in immune cells were prepared by removing epithelial cells based on gradient centrifugation. HOIL samples from three control individuals were pooled and compared with three independent HIV+ individuals. Separation was performed by Ultimate 3000LC combined with Q Exactive MS (Thermo) and screened with ESI-MS (targeted MS/MS mode). The software we used for metabolites identification is Compound Discoverer 3.1 SP1. For metabolites identification, the raw data are acquired and aligned using the Compound Discover based on the m/z value and the retention time of the ion signals. CD software offers a fully integrated suite of advanced software tools for known-parent and unknown data processing and interpretation. It is used for the initial metabolites identification. We also use mzMine2 software (with parameters of m/z tolerance=0.1 m/z ) for the online database search based on the MS1 and MS2 spectra acquired. The database used is HMDB. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | MS_Metadata.docx |
