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MB Sample ID: SA092301
| Local Sample ID: | 121_1.cdf |
| Subject ID: | SU001338 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001338 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 121_1.cdf | SA092301 | FL013211 | NSTI | Category |
| 121_1.cdf | SA092301 | FL013211 | Gr. G strep | Bacterial sp |
Collection:
| Collection ID: | CO001332 |
| Collection Summary: | EDTA plasma samples from 34 NSTI patients prospectively enrolled in the FP7 project, INFECT (Clinicaltrials.gov, NCT01790698)3 were included in this study. The patients were enrolled at 5 different clinical sites; Rigshospitalet (Copenhagen, Denmark), Karolinska University Hospital (Stockholm, Sweden), Blekingesjukhuset (Karlskrona, Sweden), Sahlgrenska University Hospital (Gothenburg, Sweden) and Haukeland University Hospital (Bergen, Norway). Sampling was done following standardized operating procedures as reported in Madsen, M. B.; Skrede, S.; Bruun, T.; Arnell, P.; Rosén, A.; Nekludov, M.; Karlsson, Y.; Bergey, F.; Saccenti, E.; Martins dos Santos, V. A. P.; et al. Necrotizing Soft Tissue Infections - a Multicentre, Prospective Observational Study (INFECT): Protocol and Statistical Analysis Plan. Acta Anaesthesiol. Scand. 2018, 62 (2), 272–279. https://doi.org/10.1111/aas.13024. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR001353 |
| Treatment Summary: | Sample preparation was performed according to A et al (A et al. 2005). In detail, 900 uL of extraction buffer (90/10 v/v methanol:water) including internal standards were added to 100 uL of sample material. The sample was shaken at 30 Hz for 3 minutes in a mixer mill and proteins were precipitated at +4 °C on ice. The sample was centrifuged at +4 °C, 14 000 rpm, for 10 minutes. 200 uL of supernatant were transferred to a micro vial and solvents were evaporated. **** Derivatization was performed according to A et al (A et al. 2005). In detail 30 uL of methoxyamine (15 ug/uL in pyridine) were added to the dry sample and the sample was shaken vigorously for 10 minutes. The reaction was begun by keeping the sample at +70 °C for 1 hour before letting the reaction proceed in room temperature for 16 hours. 30 uL of MSTFA were thenceforth added, the sample was shaken and left to react for 1 hour in room temperature. 30 μL of methyl stearate (15 ng/uL in heptane) were added before analysis. *** REFERENCES A, J., et al. (2005), 'Extraction and GC/MS Analysis of the Human Blood Plasma Metabolome', Anal. Chem., 77 (24), 8086-94. |
| Treatment Protocol Filename: | Analytical_parameters_Sleipner_10m_column_P0287_plasma.pdf |
Sample Preparation:
| Sampleprep ID: | SP001346 |
| Sampleprep Summary: | GCMS analysis was performed as described previously (A et al. 2005; Gullberg et al. 2004). In detail, 1 μL of the derivatized sample was injected in splitless mode by a CTC Combi Pal autosampler (CTC Analytics AG, Switzerland) into an Agilent 6890 gas chromatograph equipped with a 10 m x 0.18 mm fused silica capillary column with a chemically bonded 0.18 μm DB 5-MS UI stationary phase (J&W Scientific). The injector temperature was 270 °C, the purge flow rate was 20 mL min-1 and the purge was turned on after 60 seconds. The gas flow rate through the column was 1 mL min-1, the column temperature was held at 70 °C for 2 minutes, then increased by 40 °C min-1 to 320 °C, and held there for 2 minutes. The column effluent was introduced into the ion source of a Pegasus III time-of-flight mass spectrometer, GC/TOFMS (Leco Corp., St Joseph, MI, USA). The transfer line and the ion source temperatures were 250 °C and 200 °C, respectively. Ions were generated by a 70 eV electron beam at an ionization current of 2.0 mA, and 30 spectra s-1 were recorded in the mass range m/z 50 - 800. The acceleration voltage was turned on after a solvent delay of 150 seconds. The detector voltage was 1500-2000 V. |
| Sampleprep Protocol ID: | Analytical_parameters_Sleipner_10m_column_P0287_plasma.pdf |
Combined analysis:
| Analysis ID | AN002110 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus III GC |
| Column | Agilent DB 5-MS (10 m x 0.18 mm x 0.18 um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus III GC TOF |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH001540 |
| Instrument Name: | Leco Pegasus III GC |
| Column Name: | Agilent DB 5-MS (10 m x 0.18 mm x 0.18 um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001961 |
| Analysis ID: | AN002110 |
| Instrument Name: | Leco Pegasus III GC TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | Raw data from MS-files were exported from the ChromaTOF software in NetCDF format to Matlab (Mathworks, Natick, MA, USA) format; data pre-processing, such as baseline correction, chromatogram alignment, data compression and Multivariate Curve Resolution were performed using in-house custom Matlab scripts. The extracted mass spectra were identified by comparisons of their retention index and mass spectra with libraries of retention time indices and mass spectra. Mass spectra and retention index comparison was performed using NIST MS 2.0 software. Annotation of mass spectra was based on reverse and forward searches in the library. Masses and ratio between masses indicative for a derivatized metabolite were especially notified. |
| Ion Mode: | POSITIVE |
