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MB Sample ID: SA213564
| Local Sample ID: | 94_control_NB_Plasma_Quant_HILIC_Neg_88 |
| Subject ID: | SU002324 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002324 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 94_control_NB_Plasma_Quant_HILIC_Neg_88 | SA213564 | FL025992 | Sample | Type |
Collection:
| Collection ID: | CO002317 |
| Collection Summary: | Plasma samples were obtained from patients with NB at the diagnosis from peripheral venous blood collected in 3 mL EDTA K3-containing tubes, centrifuged at 4000 g for 5 min at 4 °C and stored at -80°C until analysed. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002336 |
| Treatment Summary: | - |
Sample Preparation:
| Sampleprep ID: | SP002330 |
| Sampleprep Summary: | A 50 µL aliquot of plasma was extracted adding 150 µL cold (-20 C) methanol containing as internal standard mixture of creatine (methyl-D3, 98%), vitamin B3 (D4, 98%), uracil (1,3-15N2, 98%), chenodeoxycholic acid (2,2,4,4-D4, 98%). After over-night protein precipitation, proteins were removed by centrifugation for 10 minutes at 14,000 x g and 4 °C. The supernatant was collected and stored at -80 °C until analysis when was adding to the samples a second internal standard mixture of L-alanine (13C3, 99%), chenodeoxycholic acid (2,2,4,4-D4, 98%), L-leucine (13C6, 99%), L-phenylalanine (13C6, 99%), L-tryptophan (13C11, 99%), L-tyrosine (13C6, 99%), caffeine (13C3, 99%). stearic acid, sodium salt (13C18, 98%), sodium benzoate (13C6, 99%). Quality control (QC) samples were prepared by mixing equal volumes of all the NB plasma samples. In addition, a procedural blank, used to monitor contamination acquired during all stages of sample preparation, and external quality control (EQC) samples were included in the study and were prepared in the same way as the study samples. To avoid bias due to instrument drift, the analytical study design involves analyzing the 99 samples in a randomized way, with 16 QC and 9 EQC inserted every 6 and 12 runs respectively to assess analytical precision. Subsequently, 18 identification runs and a procedural blank were analyzed. |
| Extract Storage: | -20℃ |
Combined analysis:
| Analysis ID | AN003651 | AN003652 | AN003653 | AN003654 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish |
| Column | Waters Acquity BEH C18 (150 x 2mm,1.7um) | Waters Acquity BEH C18 (100 x 2mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH002705 |
| Chromatography Summary: | Reverse phase column was eluted with 99% of mobile phase A (0.1% formic acid in water) for 0.1 min followed by a linear gradient to 100% of mobile phase B (0.1% formic acid in acetonitrile) over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 5 min. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH C18 (150 x 2mm,1.7um) |
| Flow Gradient: | 99% of A for 0.1 min followed by a linear gradient to 100% of B over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 5 min. |
| Flow Rate: | 250 µl/min |
| Injection Temperature: | 40 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Randomization Order: | yes |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002706 |
| Chromatography Summary: | Reverse phase column was eluted with 99% of mobile phase A (0.1% formic acid in water) for 0.1 min followed by a linear gradient to 100% of mobile phase B (0.1% formic acid in acetonitrile) over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 5 min. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Flow Gradient: | 99% of A for 0.1 min followed by a linear gradient to 100% of B over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 5 min. |
| Flow Rate: | 250 µl/min |
| Injection Temperature: | 40 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Randomization Order: | yes |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002707 |
| Chromatography Summary: | HILIC column was eluted at a flow rate of 200 µl/min with 90% of mobile phase B (acetonitrile) for 0.1 min followed by a linear gradient to 70% of mobile phase A ( H2O 5 mM ammonium formate, pH 3) over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 9 min. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Flow Gradient: | 90% of mobile phase B for 0.1 min followed by a linear gradient to 70% of mobile phase A over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 9 min. |
| Flow Rate: | 200 µl/min |
| Injection Temperature: | 25 |
| Solvent A: | 100% water; 5 mM ammonium formate, pH 3 |
| Solvent B: | 100% acetonitrile |
| Randomization Order: | yes |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH002708 |
| Chromatography Summary: | HILIC column was eluted at a flow rate of 200 µl/min with 90% of mobile phase B (acetonitrile) for 0.1 min followed by a linear gradient to 70% of mobile phase A ( H2O 5 mM ammonium formate, pH 3) over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 9 min. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Flow Gradient: | 90% of mobile phase B for 0.1 min followed by a linear gradient to 70% of mobile phase A over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 9 min. |
| Flow Rate: | 200 µl/min |
| Injection Temperature: | 25 |
| Solvent A: | 100% water; 5 mM ammonium formate, pH 3 |
| Solvent B: | 100% acetonitrile |
| Randomization Order: | yes |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003402 |
| Analysis ID: | AN003651 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data processing was performed using MS-DIAL for peak picking, alignment, and identification. For metabolite analysis, in house m/z and retention time libraries were used in addition to MS/MS spectra databases in msp format. MS-DIAL parameters were set as follows: MS1 tolerance, 0.05Da; MS2 tolerance, 0.025 Da; retention time begin, 0 min; retention time end, 100 min; minimum peak height, 10000; mass slice width, 0.1 Da; smoothing level, 3 scans; minimum peak width, 5 scans; sigma window value, 0.5. We considered M−H, M–H2O−H, M+Na-2H, M+Cl, M+FA-H, 2M−H, 2M+FA-H, M−2H, 3M-H adduct in negative ionization mode and M+H, M+Na, M+ACN+H, M+H–H2O, M+H–2H2O, M+2Na-H, M+ACN+Na, M+2ACN+H, 2M+H, M+2H, 2M+ACN+Na in positive ionization mode. Execute retention time correction on IS and IS kit with a RT tolerance of 0.1 min and a mass tolerance of 0.015 Da were performed. In supplementary table X all parameter settings for MS-Dial were reported. For in silico compound annotation of ion features with an acquired tandem mass spectrum MS-FINDER The MS1 and MS2 tolerances were set to 5 and 15 ppm, respectively. Formula finder were exclusively processed with C, H, O, N, P and S atoms. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003403 |
| Analysis ID: | AN003652 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data processing was performed using MS-DIAL for peak picking, alignment, and identification. For metabolite analysis, in house m/z and retention time libraries were used in addition to MS/MS spectra databases in msp format. MS-DIAL parameters were set as follows: MS1 tolerance, 0.05Da; MS2 tolerance, 0.025 Da; retention time begin, 0 min; retention time end, 100 min; minimum peak height, 10000; mass slice width, 0.1 Da; smoothing level, 3 scans; minimum peak width, 5 scans; sigma window value, 0.5. We considered M−H, M–H2O−H, M+Na-2H, M+Cl, M+FA-H, 2M−H, 2M+FA-H, M−2H, 3M-H adduct in negative ionization mode and M+H, M+Na, M+ACN+H, M+H–H2O, M+H–2H2O, M+2Na-H, M+ACN+Na, M+2ACN+H, 2M+H, M+2H, 2M+ACN+Na in positive ionization mode. Execute retention time correction on IS and IS kit with a RT tolerance of 0.1 min and a mass tolerance of 0.015 Da were performed. In supplementary table X all parameter settings for MS-Dial were reported. For in silico compound annotation of ion features with an acquired tandem mass spectrum MS-FINDER The MS1 and MS2 tolerances were set to 5 and 15 ppm, respectively. Formula finder were exclusively processed with C, H, O, N, P and S atoms. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003404 |
| Analysis ID: | AN003653 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data processing was performed using MS-DIAL for peak picking, alignment, and identification. For metabolite analysis, in house m/z and retention time libraries were used in addition to MS/MS spectra databases in msp format. MS-DIAL parameters were set as follows: MS1 tolerance, 0.05Da; MS2 tolerance, 0.025 Da; retention time begin, 0 min; retention time end, 100 min; minimum peak height, 10000; mass slice width, 0.1 Da; smoothing level, 3 scans; minimum peak width, 5 scans; sigma window value, 0.5. We considered M−H, M–H2O−H, M+Na-2H, M+Cl, M+FA-H, 2M−H, 2M+FA-H, M−2H, 3M-H adduct in negative ionization mode and M+H, M+Na, M+ACN+H, M+H–H2O, M+H–2H2O, M+2Na-H, M+ACN+Na, M+2ACN+H, 2M+H, M+2H, 2M+ACN+Na in positive ionization mode. Execute retention time correction on IS and IS kit with a RT tolerance of 0.1 min and a mass tolerance of 0.015 Da were performed. In supplementary table X all parameter settings for MS-Dial were reported. For in silico compound annotation of ion features with an acquired tandem mass spectrum MS-FINDER The MS1 and MS2 tolerances were set to 5 and 15 ppm, respectively. Formula finder were exclusively processed with C, H, O, N, P and S atoms. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003405 |
| Analysis ID: | AN003654 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data processing was performed using MS-DIAL for peak picking, alignment, and identification. For metabolite analysis, in house m/z and retention time libraries were used in addition to MS/MS spectra databases in msp format. MS-DIAL parameters were set as follows: MS1 tolerance, 0.05Da; MS2 tolerance, 0.025 Da; retention time begin, 0 min; retention time end, 100 min; minimum peak height, 10000; mass slice width, 0.1 Da; smoothing level, 3 scans; minimum peak width, 5 scans; sigma window value, 0.5. We considered M−H, M–H2O−H, M+Na-2H, M+Cl, M+FA-H, 2M−H, 2M+FA-H, M−2H, 3M-H adduct in negative ionization mode and M+H, M+Na, M+ACN+H, M+H–H2O, M+H–2H2O, M+2Na-H, M+ACN+Na, M+2ACN+H, 2M+H, M+2H, 2M+ACN+Na in positive ionization mode. Execute retention time correction on IS and IS kit with a RT tolerance of 0.1 min and a mass tolerance of 0.015 Da were performed. In supplementary table X all parameter settings for MS-Dial were reported. For in silico compound annotation of ion features with an acquired tandem mass spectrum MS-FINDER The MS1 and MS2 tolerances were set to 5 and 15 ppm, respectively. Formula finder were exclusively processed with C, H, O, N, P and S atoms. |
| Ion Mode: | NEGATIVE |
