Return to study ST000242 main page
MB Sample ID: SA011160
| Local Sample ID: | ms5047-1-3 |
| Subject ID: | SU000262 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000262 |
| 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 |
|---|---|---|---|---|
| ms5047-1-3 | SA011160 | FL002722 | Whole unconditioned medium (Defined culture media, M199) | Sample Status |
Collection:
| Collection ID: | CO000253 |
| Collection Summary: | Whole media |
| Sample Type: | Media |
Treatment:
| Treatment ID: | TR000273 |
| Treatment Summary: | Media was flash frozen with N2 and stored at -80 C. Samples can be stored at -80 C until use. ~1 ml aliquots. The following media has been provided to the metabolomics core in biological triplicates. Complete (Whole) Media:1) Whole unconditioned macrophage medium (Defined culture media, M199)2) Whole M1 macrophage medium 3) Whole M2 macrophage medium |
Sample Preparation:
| Sampleprep ID: | SP000267 |
| Sampleprep Summary: | Quality-control samples used in the study were prepared from pooled samples spiked with a selection of standards. All samples (200 μL) were thawed on ice at 4°C followed by deproteinization with methanol (1:4 ratio of plasma to methanol) and vortexed for 10 s, followed by incubation at −20°C for 2 h. The samples were then centrifuged at 15,871g for 30 min at 4°C. The supernatants were lyophilized (Savant, Holbrook, NY) and stored at −20°C prior to analysis. The samples were reconstituted in 50% H2O/acetonitrile and passed through a Microcon YM3 filter (Millipore Corporation). The supernatants were transferred to analytical vials, stored in the autosampler at 4°C, and analyzed within 48 h of reconstitution in buffer. |
Combined analysis:
| Analysis ID | AN000375 | AN000376 | AN000377 | AN000378 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters high-strength silica (150 x 2.1mm,1.8um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | TOF | TOF | TOF | TOF |
| MS instrument name | Agilent 6220 TOF | Agilent 6220 TOF | Agilent 6220 TOF | Agilent 6220 TOF |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH000271 |
| Chromatography Summary: | C18 |
| Chromatography Comments: | Metabolite separation was achieved using an Acquity UPLC system (Waters, Milford, MA) with both hydrophilic interaction chromatography (HILIC) (ethylene-bridged hybrid 2.1150 mm, 1.7 mm; Waters) and reversed-phase liquid chromatography C18 (RPLC) (high-strength silica 2.1150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a flow rate of 400 L/min. Reverse-phase chromatography was performed using 99% solvent A (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B (95% acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. The hydrophilic interaction chromatography gradient was as follows: 0 min, 100% B; 1 min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and 20 min, 100% B. The injection volume of each sample was 5 L and column was maintained at 50C. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters high-strength silica (150 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000321 |
| Analysis ID: | AN000375 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | C18-PESI (+ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | POSITIVE |
| MS ID: | MS000322 |
| Analysis ID: | AN000376 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | C18-NESI (-ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS000323 |
| Analysis ID: | AN000377 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | HILIC-PESI (+ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | POSITIVE |
| MS ID: | MS000324 |
| Analysis ID: | AN000378 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | HILIC-NESI (-ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | NEGATIVE |
