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.

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Study IDST002498
Study TitlePlasma Metabolomics Profiling of 580 Patients from the Weill Cornell Medicine Early Detection Research Network Prostate Cancer Cohort
Study SummaryProstate 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 NameKrumsiek
First NameJan
Address1305 York Avenue, New York, NY 10021
Emailjak2043@med.cornell.edu
Phone646-962-4152
Submit Date2023-02-24
Total Subjects580
Num Males580
Analysis Type DetailLC-MS
Release Date2023-09-19
Release Version1
Jan Krumsiek Jan Krumsiek
https://dx.doi.org/10.21228/M86H7K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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

Chromatography:

Chromatography ID:CH003503
Instrument Name:Waters Acquity
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 5% B to 80% B over 3.35 minutes.
Flow Rate:0.35 mL/min
Solvent A:0.1% formic acid and 0.05% PFPA in water, pH ~2.5
Solvent B:0.1% formic acid and 0.05% PFPA in methanol, pH ~2.5
Chromatography Type:Reversed phase
  
Chromatography ID:CH003504
Instrument Name:Waters Acquity
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes.
Flow Rate:0.60 mL/min
Solvent A:0.1% formic acid and 0.05% PFPA in water, pH ~2.5
Solvent B:0.1% formic acid and 0.05% PFPA in 50% methanol / 50% acetonitrile, pH ~2.5
Chromatography Type:Reversed phase
  
Chromatography ID:CH003505
Instrument Name:Waters Acquity
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes.
Flow Rate:0.35 mL/min
Solvent A:6.5 mM ammonium bicarbonate in water, pH 8
Solvent B:6.5 mM ammonium bicarbonate in 95% methanol / 5% water
Chromatography Type:Reversed phase
  
Chromatography ID:CH003506
Instrument Name:Waters Acquity
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes.
Flow Rate:0.50 mL/min
Solvent A:10 mM ammonium formate in 15% water / 5% methanol / 80% acetonitrile (effective pH 10.16 with NH4OH)
Solvent B:10 mM ammonium formate in 50% water / 50% acetonitrile (effective pH 10.60 with NH4OH)
Chromatography Type:HILIC
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