Return to study ST001929 main page
MB Sample ID: SA178532
| Local Sample ID: | 180731bJWsa03_2 |
| Subject ID: | SU002007 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002007 |
| 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 |
|---|---|---|---|---|
| 180731bJWsa03_2 | SA178532 | FL022254 | B393u8.2_040 | Subject |
| 180731bJWsa03_2 | SA178532 | FL022254 | C1 | treatment |
Collection:
| Collection ID: | CO002000 |
| Collection Summary: | Urine biospecimens were collected during cross-over trial among premenopausal women conducted from 2007-2010, and details about the study design and population are published elsewhere (Morimoto et al 2014; Maskarinec et al 2011; Maskarinec et al 2012). The BEAN2 trial was a cross-over study with six months on a high- and a low-soy diet, each separated by a 1-month washout period. The objective of the study was to evaluate soy intake and nipple aspirate fluid, a possible indicator of breast cancer risk. Eligibility criteria for the parent study included a normal mammogram, no oral contraceptives, not pregnant, no previous cancer diagnosis or breast surgery, regular menstrual periods, low soy intake, and the ability to produce nipple aspirate fluid. There were 84 women from the original trial who had eight stored urine samples over the cross-over intervention, from which 60 samples were selected for metabolomics analysis. |
| Sample Type: | Urine |
Treatment:
| Treatment ID: | TR002019 |
| Treatment Summary: | As part of the parent study, daidzein, equol, and ODMA concentrations were analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) as detailed elsewhere (Franke et al 2009). These previously measured concentrations were used to classify metabotypes. Each urine sample was identified as being ODMA producer/non-producer and equol producer/non-producer based on a cut-off of equol/ODMA:daidzein ratio of 0.018 (36). All samples, except two samples, which were excluded from selection, had daidzein concentrations >2 nmol/mg creatinine, indicating sufficient presence of the precursor metabolite for metabolite detection. |
Sample Preparation:
| Sampleprep ID: | SP002013 |
| Sampleprep Summary: | Urine samples were stored at -80C. |
Combined analysis:
| Analysis ID | AN003137 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus IV GC |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus IV TOF |
| Ion Mode | POSITIVE |
| Units | Peak height |
Chromatography:
| Chromatography ID: | CH002319 |
| Chromatography Summary: | Urine samples were analyzed by the National Institutes of Health (NIH) West Coast Metabolomics Center in the Fiehn laboratory, using established protocols and more detail on these protocols are available elsewhere (Fiehn et al 2008). To consider broad aspects of metabolism relevant to diet, primary metabolism and biogenic amines platforms were evaluated. In brief, primary metabolism metabolites were assayed using automated liner exchange-cold injection system, gas chromatography-time of flight mass spectrometry (ALEX-CIS GCTOF). |
| Instrument Name: | Leco Pegasus IV GC |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002917 |
| Analysis ID: | AN003137 |
| Instrument Name: | Leco Pegasus IV TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | fter hard ionization by electron ionization, one electron gets abstracted from the intact molecules which hence become positively charged. The standardized -70 eV ionization voltage is so high that molecules fragment into multiple product ions, which may also form rearrangements among each other. Fragments are then analyzed by time of flight mass spectrometry which is made here by the vendor Leco corporation not to obtain accurate mass information at high resolution but instead to obtain mass spectra at very high sensitivity and speed. Mass spectrometry parameters are used as follows: a Leco Pegasus IV mass spectrometer is used with unit mass resolution at 17 spectra s-1 from 80-500 Da at -70 eV ionization energy and 1800 V detector voltage with a 230°C transfer line and a 250°C ion source. |
| Ion Mode: | POSITIVE |
