Return to study ST001317 main page
MB Sample ID: SA094973
| Local Sample ID: | C-1Q4S6-U-00 |
| Subject ID: | SU001391 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001391 |
| 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-1Q4S6-U-00 | SA094973 | FL013533 | CHEAR Study Sample | SampleType |
Collection:
| Collection ID: | CO001386 |
| Collection Summary: | All study participants provide 4 individual urine samples corresponding to 4 unique time points: 2 pre intervention and 2 post-intervention samples. The first of these 4 urine samples are from an afternoon/evening clinic visit at baseline, and the remaining 3 urine samples are first morning voids. All materials for urine sample collection are phthalate-free. All have been stored in a -20 freezer in the field, then transfered on dry ice to UW -20 freezer equipped with temperature alarms. Samples have not yet been thawed. |
| Sample Type: | Urine |
| Storage Conditions: | -20℃ |
Treatment:
| Treatment ID: | TR001406 |
| Treatment Summary: | HAPI is a randomized controlled trial with subject recruitment utilizing an existing community health worker delivered asthma education program operated by the region's federally qualified health center. HAPI eligibility criteria includes: (i) age 6 – 12 years, (ii) asthma not well controlled, (iii) no household smokers, and (iv) residence within 400m of dairy/crop production. Recruited subjects are randomized to a standard educational program or an enhanced intervention, which includes 2 portable room HEPA cleaners – one in the child sleeping area and one in the living room – with PM and ammonia (NH3) reduction filters. Enrollment occurs on a rolling basis, and each subject undergoes an initial baseline clinic visit and three additional health assessment in-home visits – the first and last of which occurring alongside environmental sampling. Subjects are randomized after the first home visit. Subjects in the control (standard asthma education only) group will receive HEPA cleaners at the end of their study year, if requested. The study setting is Yakima County, WA. |
Sample Preparation:
| Sampleprep ID: | SP001399 |
| Sampleprep Summary: | Urine samples were thawed on ice, vortexed, and specific gravity (SpG) was measured. Samples were diluted with LC-MS grade water to the lowest measured SpG with ultrapure water (HILIC-positive only). Aliquots of 20 μL of the diluted urine were prepared for analysis with the LC-HRMS. A third 20 μL aliquot from each sample was combined for use as a pooled quality control sample (‘LQC’). When aliquoting was complete, the LQC sample was re-aliquoted into 20μL samples. All aliquots were returned to -80°C until analysis. Extraction was performed immediately prior to LC-HRMS analysis. All sample aliquots were thawed on ice, combined with 180uL of acetonitrile containing internal standards. Samples were then centrifuged and 80μL of supernatant transferred to an LC vial for analysis. Following the same protocol matrix blank (replacing the urine with H2O) and multiple LQCs were extracted. |
| Processing Storage Conditions: | On ice |
Combined analysis:
| Analysis ID | AN002192 | AN002193 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um,100 Å) | Agilent Zorbax Eclipse Plus C18, RRHD (50 × 2.1 mm,1.8 um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6550 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak Intensity | Peak Intensity |
Chromatography:
| Chromatography ID: | CH001607 |
| Chromatography Summary: | Sample extracts were analyzed using an ultra-high performance liquid chromatography (UHPLC) 1290 Infinity II system (including 0.3 µm inline filter, Agilent Technologies, Santa Clara, USA) with 1260 Infinity II isocratic pump (including 1:100 splitter) coupled to a 6550 iFunnel quadrupole-time time of flight (Q-TOF) mass spectrometer with a dual AJS electrospray ionization source (Agilent Technologies, Santa Clara, USA). Samples were maintained at 5C in the autosampler module. For polar metabolites separation, 2 uL of sample was injected onto a HILIC SeQuant® ZIC®-HILIC column (100 mm × 2.1 mm, 100 Å, 3.5 µm particle size, Merck, Darmstadt, Germany) with a guard fitting (14 mm × 1 mm, 5.0 µm particle size, Merck, Darmstadt, Germany) maintained at 25C. Separation occurred using Mobile phase A consisted of water with 0.1% formic acid and Mobile phase B consisted of Acetonitrile with 0.1% formic acid at a flow rate of 0.3 ml/min as described in Table 1. Data was acquired with a mass range of 40-1200 m/z. Solvent gradients were as follows: 95% solvent B, hold for 1.5 min; linear decrease to 40% solvent B at 12 minutes; hold for 2 min, linear decrease to 25% solvent B at 14.2 min, hold for 2.8 min; increase to 95% solvent B at 18 min, hold for 7 min. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um,100 Å) |
| Column Temperature: | 25C |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Analytical Time: | 25 min |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001608 |
| Chromatography Summary: | Sample extracts were analyzed using an ultra-high performance liquid chromatography (UHPLC) 1290 Infinity II system (including 0.3 µm inline filter, Agilent Technologies, Santa Clara, USA) with 1260 Infinity II isocratic pump (including 1:100 splitter) coupled to a 6550 iFunnel quadrupole-time time of flight (Q-TOF) mass spectrometer with a dual AJS electrospray ionization source (Agilent Technologies, Santa Clara, USA). Samples were maintained at 5C in the autosampler module. For nonpolar metabolites separation, 2 uL of sample sandwiched between 10 uL of water was injected onto a Zorbax Eclipse Plus C18, RRHD column (50 mm × 2.1 mm, 1.8 µm particle size, Agilent Technologies, Santa Clara, USA) coupled to a guard column (5 mm × 2 mm, 1.8 µm Agilent Technologies, Santa Clara, USA) maintained at 50C. Separation occurred using Mobile phase A consisted of water with 0.1% formic acid and Mobile phase B consisted of 2-propanol:ACN (90:10, v/v) with 0.1% formic acid at a flow rate of 0.4 ml/min as described in Table 2. Data was acquired with a mass range of 50-1200 m/z. Solvent gradients were as follows: 5% solvent B; linear increase to 98% solvent B at 13.5 min, hold for 1.5 min; decrease to 5% solvent B at 15.5 min, hold for 3.5 min. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent Zorbax Eclipse Plus C18, RRHD (50 × 2.1 mm,1.8 um) |
| Column Temperature: | 50C |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid |
| Analytical Time: | 19 min |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002039 |
| Analysis ID: | AN002192 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Analysis was performed for all batches (6) in each mode. 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. We also included the Specific gravity measurements and dilution factor performed for each sample prior to data acquisition. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 250C |
| Capillary Voltage: | 3000 |
| MS ID: | MS002040 |
| Analysis ID: | AN002193 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Analysis was performed for all batches (6) in each mode. 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. We also included the Specific gravity measurements and dilution factor performed for each sample prior to data acquisition. |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 250C |
| Capillary Voltage: | -3000 |
