Return to study ST001662 main page
MB Sample ID: SA152170
| Local Sample ID: | mv08618_26.mzXML |
| Subject ID: | SU001739 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Pooled |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001739 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Pooled |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| mv08618_26.mzXML | SA152170 | FL017890 | TAG3 | Disease |
| mv08618_26.mzXML | SA152170 | FL017890 | NMIBC | Type of tumor |
Collection:
| Collection ID: | CO001732 |
| Collection Summary: | Study subjects Sixty-four BC patients were recruited between May 2016 and April 2018 at La Fe University and Polytechnic Hospital (Valencia, Spain). Twenty age- and sex-matched healthy volunteers (control group) who underwent an ultrasound scan to rule out the presence of urological malignancies or other alterations were also recruited. Patients and controls were clinically followed-up until May 2020. Pre-operative clinical staging was performed through physical examination, urine cytology and CT scans of the chest, abdomen and pelvis (in case of invasive bladder cancer). The tumor histological classification was done according to grade in the WHO 1973 and 2004 classifications. Demographic and clinical data were collected. The exclusion criteria were lack of informed consent, absence of histological confirmation and presence of other malignancies. Informed consent was obtained from all participants according to protocols approved by the ethics review board at La Fe University and Polytechnic Hospital. The study was performed according to the declaration of Helsinki, as amended in Edinburgh in 2000. Urine collection A first morning urine sample of 25-50 ml was collected in sterile containers from all participants. Urine was kept at 4 ºC until processing and centrifuged at 805 x g for 5 min at 4 ºC to remove cellular debris. Supernatant was aliquoted and frozen at -80 ºC until analyzed. The concentration of creatinine in each urine sample was measured by clinical laboratory standardized methods. |
| Sample Type: | Urine |
Treatment:
| Treatment ID: | TR001752 |
| Treatment Summary: | A first morning urine sample of 25-50 ml was collected in sterile containers from all participants. Urine was kept at 4 ºC until processing and centrifuged at 805 x g for 5 min at 4 ºC to remove cellular debris. Supernatant was aliquoted and frozen at -80 ºC until analyzed. The concentration of creatinine in each urine sample was measured by clinical laboratory standardized methods |
Sample Preparation:
| Sampleprep ID: | SP001745 |
| Sampleprep Summary: | Sample treatment was performed according to a previous study 22. Briefly, after centrifugation, 40 µl of urine cleaned supernatant were transferred to a 96 well-plate for LC-MS (liquid chromatography-mass spectrometry) analysis and diluted by adding 50 µl of H2O (0.1 % v/v HCOOH). Each sample was spiked with 10 µl of 20 µM IS solution containing phenylalanine-d5, caffeine-d9, leukine enkephaline and reserpine in H2O:CH3OH (1:1, 0.1% v/v HCOOH). Blank samples were prepared by replacing urine by ultrapure H2O. A quality control (QC) sample was prepared by mixing 10 µl from each urine sample. |
Combined analysis:
| Analysis ID | AN002713 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 6550 |
| Column | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| MS Type | EI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6550 QTOF |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH002002 |
| Chromatography Summary: | The metabolomic analysis was carried out using an Ultra-Performance Liquid Chromatography (UPLC) system coupled to an iFunnel Q-ToF (quadrupole-time-of-flight) Agilent 6550 mass spectrometer (Agilent Technologies, CA, USA) using an UPLC BEH C18 (100 x 2.1 mm, 1.7 µm, Waters, Wexford, Ireland) column from Waters (Wexford, Ireland). Autosampler and column temperatures were set to 4 °C and 40 °C, respectively, and the injection volume was 5 µl. Mobile phase A and mobile phase B consisted of H2O and acetonitrile, both containing 0.1% of formic acid. A gradient elution was performed at a flow rate of 400 µl min-1 along 14 min as follows: initial conditions of 98% of mobile phase A was maintained for 1 min, and then decreased until 75% in 2 min, 50% in 3 min and 5% in 3 more min. 95% of mobile phase B was held for 3 min and then, a 0.55 min gradient was used to return to the initial conditions, which were held for 2.5 min to totally column recovery. |
| Instrument Name: | Agilent 6550 |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | initial conditions of 98% of mobile phase A was maintained for 1 min, and then decreased until 75% in 2 min, 50% in 3 min and 5% in 3 more min. 95% of mobile phase B was held for 3 min and then, a 0.55 min gradient was used to return to the initial conditions, which were held for 2.5 min to totally column recovery |
| Flow Rate: | 400ul/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002510 |
| Analysis ID: | AN002713 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | EI |
| MS Comments: | Full scan MS data from 50 to 1700 m/z with a scan frequency of 6 Hz was collected both in positive (ESI+) and negative (ESI-) electrospray ionization modes. The following electrospray ionization parameters were used: gas temperature, 200 °C; drying gas, 14 l min-1; nebulizer, 60 psi; sheath gas temperature, 350 °C; sheath gas flow, 11 l min-1. Urine samples were randomly injected in the chromatographic system in order to avoid intra-batch variability, as well as to enhance quality and reproducibility. QC sample was analyzed every 7 injections to monitor and correct changes in the instrument response. QC sample was also repeatedly analysed under auto MS/MS and All-ion (MSE) fragmentation modes to provide useful information of fragment ions for identification purposes. Sample stability and analytical drift were investigated through IS intensities. Blank analysis was performed at the end of the sequence and used to identify artefacts from sampling, preparation of samples and analysis. |
| Ion Mode: | POSITIVE |
