Summary of Study ST002498
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001613. The data can be accessed directly via it's Project DOI: 10.21228/M86H7K This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002498 |
| Study Title | Plasma Metabolomics Profiling of 580 Patients from the Weill Cornell Medicine Early Detection Research Network Prostate Cancer Cohort |
| Study Summary | Prostate cancer is the second most common cancer in men and affects 1 in 9 men in the United States. Early screening for prostate cancer often involves monitoring levels of prostate-specific antigen (PSA) and performing digital rectal exams. However, a prostate biopsy is always required for definitive cancer diagnosis. The Early Detection Research Network (EDRN) is a consortium within the National Cancer Institute aimed at improving screening approaches and early detection of cancers. As part of this effort, the Weill Cornell EDRN Prostate Cancer has collected and biobanked specimens from men undergoing a prostate biopsy between 2008 and 2017. In this report, we describe blood metabolomics measurements for a subset of this population. The dataset includes detailed clinical and prospective records for 580 patients who underwent prostate biopsy, 287 of which were subsequentially diagnosed with prostate cancer, combined with profiling of 1,482 metabolites from plasma samples collected at the time of biopsy. We expect this dataset to provide a valuable resource for scientists investigating prostate cancer metabolism. |
| Institute | Weill Cornell Medicine |
| Last Name | Krumsiek |
| First Name | Jan |
| Address | 1305 York Avenue, New York, NY 10021 |
| jak2043@med.cornell.edu | |
| Phone | 646-962-4152 |
| Submit Date | 2023-02-24 |
| Total Subjects | 580 |
| Num Males | 580 |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-09-19 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004654 | AN004655 | AN004656 | AN004657 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | peak area | peak area | peak area | peak area |
MS:
| MS ID: | MS004401 |
| Analysis ID: | AN004654 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos early). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | preprocessing_workflow.docx |
| MS ID: | MS004402 |
| Analysis ID: | AN004655 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos late). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | preprocessing_workflow.docx |
| MS ID: | MS004403 |
| Analysis ID: | AN004656 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Neg). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | preprocessing_workflow.docx |
| MS ID: | MS004404 |
| Analysis ID: | AN004657 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Polar). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | preprocessing_workflow.docx |
