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MB Sample ID: SA157085
| Local Sample ID: | C-23GB0-BR-00 |
| Subject ID: | SU001769 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001769 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| C-23GB0-BR-00 | SA157085 | FL018370 | Study_Sample | Class |
Collection:
| Collection ID: | CO001762 |
| Collection Summary: | The study includes archived biological samples collected during pregnancy (maternal blood, urine, and hair), birth (infant cord blood, placenta, and meconium), and childhood (urine, blood, buccal cells, breast milk, toenails, and stool), and further health outcomes are being assessed through DNA methylation arrays, gene expression, microbiome sequencing, metabolomics and flow cytometry of these samples. Breast milk samples were collected at home by study participants from unsterilized bilateral breasts, with separate study-provided sterile collection bottles used for milk from each breast. To capture a representative portrait of infant exposure during breastfeeding we did not use a sterile collection protocol. Subjects provided a minimum of 18 mL and up to 80 mL of milk from each breast, with a median of 35 mL per breast. Samples were stored in the refrigerator at participants homes for up to approximately 1 day, brought in cold packs to the postpartum follow-up appointment (between 3.7 and 12 weeks after delivery), and immediately chilled. Samples were processed within 24 h of receipt. Samples were stored at -80C until analysis |
| Sample Type: | Breast milk |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001782 |
| Treatment Summary: | Study subjects were from the New Hampshire Birth Cohort Study (NHBCS). Eligible participants for this birth cohort are pregnant women between the ages of 18 and 45 years who report using a private well for their home water source and are receiving prenatal care in clinics in New Hampshire, United States, as previously described (Gilbert-Diamond et al., 2011; Farzan et al., 2013). Subjects were recruited between approximately 24 and 28 weeks of gestation at routine prenatal visits. The Center for the Protection of Human Subjects at Dartmouth gave institutional review board approval, and all methods were performed according to guidelines. All subjects gave written informed consent for participation for themselves and their infants. The study is observational, and no treatment occurred. |
Sample Preparation:
| Sampleprep ID: | SP001775 |
| Sampleprep Summary: | Prior to sample preparation, breast milk samples were thawed on ice and then vortexed thoroughly to prevent separation of lipid-rich and aqueous phases. Extracts were prepared by treating 75μL of breastmilk sample with 150μL of LC-MS grade acetonitrile containing a series of XX 13C-labelled internal standards (listed below), vortexed, and allowed to equilibrate at 4C for 30 minutes. The extract was then centrifuged for 10 mins at 18,1000 x g and 4C, and 50μL of extract was transferred to an LC autosampler vial containing 50μL of water and placed in a refrigerated autosampler until analysis. Following the same protocol, for each batch matrix blank (replacing the breast milk with H2O) and multiple QAQC samples were extracted. Internal standards used include [13C3]-Cortisol, [13C6]-NNAL, [trimethyl-13C3]-caffeine, [13C8]-PFOA, [13C8]-PFOS, [13C5]-L-methionine, [13C3]-Cotinine, [13C9, 15N]-L-tyrosine, [13C5, 15N]-L-glutamic acid, [13C3]-glyphosate, [13C6]-D-glucose, [13C9]-PFNA, [13C6]-PFHxA, [13C6]-PFHxS, [13C9]-PFDeA and [13C9]-PFUDeA, and were added at levels comparable to those in human plasma samples. |
| Processing Storage Conditions: | 4℃ |
| Extraction Method: | Protein precipitation with acetontrile. |
Combined analysis:
| Analysis ID | AN002762 | AN002763 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Higgins Analytical Targa C18 (50 x 2.1mm,5um) | Higgins Analytical Targa C18 (50 x 2.1mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q-Exactive HFX | Thermo Q-Exactive HFX |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak intensity | Peak intensity |
Chromatography:
| Chromatography ID: | CH002042 |
| Chromatography Summary: | Sample extracts were analyzed using an ultra-high performance liquid chromatography (UHPLC) equipped with dual pumps for both C18-pos and C18-negative analysis uysing a Thermo Scientific Vanquish Duo LC interfaced to a Thermo Scientific Q-Exactive HFX with electrospray ionization source operated in positive mode. Samples were maintained at 4C in the autosampler module. For C18-pos separation, 5 uL of sample was injected onto a C18 columns (50 mm × 2.1 mm, 5 µm particle size, Higgins Analytical Inc) maintained at 30C. 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. Flow rate was held at at 0.4 ml/min for 1.5 mins, and increased to 0.5 ml/min. Solvent gradients were as follows: 85% solvent A, hold for 1.5 min; linear decrease to 5% solvent A at 5 minutes; hold for 2.5 min, for a total run time of 7.5 min Data was acquired with a mass range of 85-1275 m/z. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Higgins Analytical Targa C18 (50 x 2.1mm,5um) |
| Column Temperature: | 30C |
| Flow Rate: | 0.4-0.5 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Analytical Time: | 7.5 min |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002043 |
| Chromatography Summary: | Sample extracts were analyzed using an ultra-high performance liquid chromatography (UHPLC) equipped with dual pumps for both C18-pos and C18-negative analysis using a Thermo Scientific Vanquish Duo LC interfaced to a Thermo Scientific Q-Exactive HFX with electrospray ionization source operated in negative mode. Samples were maintained at 4C in the autosampler module. For C18-neg separation, 5 uL of sample was injected onto a C18 columns (50 mm × 2.1 mm, 5 µm particle size, Higgins Analytical Inc) maintained at 30C. Separation occurred using Mobile phase A consisted of water with 10mM ammonium acetate and Mobile phase B consisted of Acetonitrile. Flow rate was held at at 0.4 ml/min for 1.5 mins, and increased to 0.5 ml/min. Solvent gradients were as follows: 85% solvent A, hold for 1.5 min; linear decrease to 5% solvent A at 5 minutes; hold for 2.5 min, for a total run time of 7.5 min Data was acquired with a mass range of 85-1275 m/z. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Higgins Analytical Targa C18 (50 x 2.1mm,5um) |
| Column Temperature: | 30C |
| Flow Rate: | 0.4-0.5 mL/min |
| Solvent A: | 100% water; 10mM ammonium acetate |
| Solvent B: | 100% acetonitrile |
| Analytical Time: | 7.5 min |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002559 |
| Analysis ID: | AN002762 |
| Instrument Name: | Thermo Q-Exactive HFX |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Analysis was performed for all batches 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 feature tables were generated by converting .RAW files to mzXML, and extracted using apLCMS at 5 different peak detection parameters. The resulting tables were merged using xMSanalyzer to remove redundant peaks, and batch corrected using ComBAT. All scripts for data extraction are included in the raw datafile uploads. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 300 |
| Capillary Voltage: | 35 (S-Lens RF) |
| Dry Gas Flow: | 45 |
| Ionization: | Postive |
| Source Temperature: | 250 |
| Spray Voltage: | 3500 |
| Processing Parameters File: | apLCMSv6.6.8_runscript_c18-pos_HRE0010_02Dec2020.r xMSanalyzer_v2.0.8_HRE0010-C18pos_18Dec2020.r |
| MS ID: | MS002560 |
| Analysis ID: | AN002763 |
| Instrument Name: | Thermo Q-Exactive HFX |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Analysis was performed for all batches 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 feature tables were generated by converting .RAW files to mzXML, and extracted using apLCMS at 5 different peak detection parameters. The resulting tables were merged using xMSanalyzer to remove redundant peaks, and batch corrected using ComBAT. All scripts for data extraction are included in the raw datafile uploads. |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 300 |
| Capillary Voltage: | 4000 (S-Lens RF) |
| Dry Gas Flow: | 45 |
| Ionization: | Negative |
| Source Temperature: | 250 |
| Spray Voltage: | -4000 |
| Processing Parameters File: | apLCMSv6.6.8_runscript_c18-neg_HRE0010_02Dec2020.r xMSanalyzer_v2.0.8_HRE0010-C18neg_18Dec2020.r |
