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MB Sample ID: SA101364
| Local Sample ID: | C-1STL5-U-00 |
| Subject ID: | SU001459 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001459 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| C-1STL5-U-00 | SA101364 | FL014225 | sample | Factor |
Collection:
| Collection ID: | CO001454 |
| Collection Summary: | Samples were received and stored at -80°C until processing. In total, 315 samples had sufficient sample volume for metabolomics analysis. |
| Collection Protocol Filename: | Report_Michels__2017_1977.docx |
| Sample Type: | Urine |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001474 |
| Treatment Summary: | See report |
| Treatment Protocol Filename: | Report_Michels__2017_1977.docx |
Sample Preparation:
| Sampleprep ID: | SP001467 |
| Sampleprep Summary: | Aliquoting was initially performed for all CHEAR assays, and included an aliquot of each sample for metabolomics and specific gravity measurements. Specific gravity measurements were made first, to determine dilution factors required for pre-acquisition normalization. Specific gravity and dilution factors are included in the “Meta_2019_Michels2017_1977.csv” Urine samples were thawed on ice in batches of approximately 65 samples, and vortexed. The sample was diluted with water down to a specific gravity of 1.002 for pre-acquisition normalization. A 20 L aliquot of the diluted sample was prepared for metabolomics analysis. In addition, a 20 L aliquot from each diluted sample was combined for use as a pooled quality control sample and re-aliquoted into 20L samples. Samples were then returned to -80°C until analysis. Extraction was performed in batches of approximately 65 samples, immediately prior to LC-HRMS analysis. All samples in a batch were thawed on ice, combined with 180L of acetonitrile containing internal standards, and vortexed for 30sec. Samples were then centrifuged (13000 g, 15 min, °C), and 60 L of supernatant transferred to two LC vials for RP and HILIC analysis. Extract remainder was returned to -80°C. Following the same protocol 20 L aliquots each of a matrix blank (replacing the urine with H2O, “matrix”), a CHEAR Reference urine sample (global quality control, “UT”), a NIST 3672 sample (global quality control, “NIST”), and multiple pooledQC samples (local quality control, “LQC”) were extracted. |
| Sampleprep Protocol Filename: | Report_Michels_ 2017_1977.docx |
Combined analysis:
| Analysis ID | AN002312 | AN002313 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | HILIC |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1 mm,1.8 µm) | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6550 QTOF | Agilent 6545 QTOF |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | area | area |
Chromatography:
| Chromatography ID: | CH001699 |
| Chromatography Summary: | Reverse Phase Gradient separation |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1 mm,1.8 µm) |
| Column Temperature: | 25°C |
| Flow Rate: | 0.4 mL/min |
| Sample Injection: | 2uL |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001700 |
| Chromatography Summary: | HILIC Gradient separation |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| Column Temperature: | 25°C |
| Flow Rate: | 0.3 mL/min |
| Sample Injection: | 2uL |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002155 |
| Analysis ID: | AN002312 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Database dependent targeted identification: Metabolites were identified based upon in-house database matching considering retention time, accurate mass, and MSMS matching (when available) matching with pure standards analyzed under the same conditions. Untargeted metabolomics analysis: Parameters for peak picking grouping, and alignment with ‘XCMS’ included centwave feature detection, orbiwarp retention time correction, minimum fraction of samples in one group to be a valid group = 0.25, isotopic ppm error = 10. Width of overlapping m/z slices (mzwid) = 0.003 or 0.015, and retention time window (bw) = 12.4 s and 22 s for ZHP and RPN, respectively. Minimum and maximum peak width were 5 and 20 s for reverse phase and 10 and 60 s for HILIC. The resulting peak table of retention times, m/z values, and peak areas was exported for data processing. Annotation of the untargeted data was facilitated by xMSannotator using the annotation scheme of Schymanski et al. (Environmental Science & Technology, 2014). Level 1 and 2 annotations were those that were confirmed with database dependent annotation. Lower confidence annotations (level 4) are those from the HMDB and T3DB online databases that were highly ranking by xMSannotator. Level 5 annotations were named by “mz_rt”. Metadata for the analysis including the batch and run order of each injection are provided in the Metafile, “Meta_2019_Michels2017_1977.csv”. We also included the Specific gravity measurements and dilution factor performed for each sample prior to data acquisition. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002156 |
| Analysis ID: | AN002313 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Database dependent targeted identification: Metabolites were identified based upon in-house database matching considering retention time, accurate mass, and MSMS matching (when available) matching with pure standards analyzed under the same conditions. Untargeted metabolomics analysis: Parameters for peak picking grouping, and alignment with ‘XCMS’ included centwave feature detection, orbiwarp retention time correction, minimum fraction of samples in one group to be a valid group = 0.25, isotopic ppm error = 10. Width of overlapping m/z slices (mzwid) = 0.003 or 0.015, and retention time window (bw) = 12.4 s and 22 s for ZHP and RPN, respectively. Minimum and maximum peak width were 5 and 20 s for reverse phase and 10 and 60 s for HILIC. The resulting peak table of retention times, m/z values, and peak areas was exported for data processing. Annotation of the untargeted data was facilitated by xMSannotator using the annotation scheme of Schymanski et al. (Environmental Science & Technology, 2014). Level 1 and 2 annotations were those that were confirmed with database dependent annotation. Lower confidence annotations (level 4) are those from the HMDB and T3DB online databases that were highly ranking by xMSannotator. Level 5 annotations were named by “mz_rt”. Metadata for the analysis including the batch and run order of each injection are provided in the Metafile, “Meta_2019_Michels2017_1977.csv”. We also included the Specific gravity measurements and dilution factor performed for each sample prior to data acquisition. |
| Ion Mode: | POSITIVE |
