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

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001613
Project DOI:doi: 10.21228/M86H7K
Project Title:Plasma Metabolomics Profiling of 580 Patients from the Weill Cornell Medicine Early Detection Research Network Prostate Cancer Cohort
Project Summary:Metabolomics profiling of 580 patients who underwent prostate biopsy from plasma samples taken at the time of biopsy.
Institute:Weill Cornell Medicine
Last Name:Krumsiek
First Name:Jan
Address:1305 York Avenue, New York, NY 10021
Email:jak2043@med.cornell.edu
Phone:646-962-4152

Subject:

Subject ID:SU002954
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Diagnosis
SA307637C003630
SA307638C003620
SA307639C006990
SA307640C006960
SA307641C003610
SA307642C006930
SA307643C003710
SA307644C003700
SA307645C003680
SA307646C003580
SA307647C003650
SA307648C007000
SA307649C003460
SA307650C003440
SA307651C007040
SA307652C007070
SA307653C003480
SA307654C003510
SA307655C007020
SA307656C003530
SA307657C003520
SA307658C003720
SA307659C003730
SA307660C003940
SA307661C006810
SA307662C006820
SA307663C003900
SA307664C006790
SA307665C006750
SA307666C006700
SA307667C006730
SA307668C003990
SA307669C003890
SA307670C006830
SA307671C003790
SA307672C006880
SA307673C003760
SA307674C003750
SA307675C003810
SA307676C003820
SA307677C003860
SA307678C003840
SA307679C006850
SA307680C003380
SA307681C003340
SA307682C007590
SA307683C002850
SA307684C002830
SA307685C002820
SA307686C007550
SA307687C007540
SA307688C002940
SA307689C002920
SA307690C002910
SA307691C002810
SA307692C002800
SA307693C002710
SA307694C002690
SA307695C002680
SA307696C002670
SA307697C002740
SA307698C007630
SA307699C002790
SA307700C002780
SA307701C002770
SA307702C007520
SA307703C002990
SA307704C003270
SA307705C007230
SA307706C003240
SA307707C007310
SA307708C003280
SA307709C003290
SA307710C003320
SA307711C007220
SA307712C003300
SA307713C003160
SA307714C007320
SA307715C003040
SA307716C007480
SA307717C007500
SA307718C003010
SA307719C003070
SA307720C003080
SA307721C003140
SA307722C003110
SA307723C003090
SA307724C004020
SA307725C004030
SA307726C005070
SA307727C005060
SA307728C006030
SA307729C006040
SA307730C005110
SA307731C005170
SA307732C005210
SA307733C005190
SA307734C005980
SA307735C005030
SA307736C005020
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Collection:

Collection ID:CO002947
Collection Summary:The Weill Cornell EDRN Prostate Cancer Cohort consented and recruited 1,144 patients (518 cases and 626 controls) over 9 years (from 2008 to 2017). In order to be eligible for the study, patients needed to be adult males, have no prior history of prostate cancer or prostate biopsies, and be scheduled to undergo prostate biopsy at Weill Cornell Medicine in New York City. Need of prostate biopsy was determined based on suspicion of prostate cancer, which primarily included elevated PSA levels, abnormal digital rectal exam (DRE) results, or suspicious findings based on imaging. Prostate biopsies included at least 10 cores taken in a laterally directed fashion, and a fasting blood sample was collected prior to prostate biopsy from all recruited patients. Biopsy tissue, together with urine and blood samples were processed and biobanked at Weill Cornell Medicine. For each patient, extensive clinical parameters were collected, including biopsy results, prostate cancer diagnosis and 2-year follow-up clinical information. EDTA-plasma samples for metabolomics profiling were selected to include patients with complete 12- and 24-months follow-up information available (see Data Records section for more details). This subset included a total of 580 patients, with 267 men diagnosed with PCa and 313 controls.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002963
Treatment Summary:Fasting blood was collected prior to biopsy in 6ml BD Vacutainer® EDTA tubes. Immediately after blood draw, the tube was inverted 8-10 times to mix the additive with the blood and placed immediately on ice. Tubes were centrifuged at 2,500 rpm for 15 minutes at 4°C within two hours of blood collection. Plasma aliquots of 100ul or 200ul were extracted from the top layer, transferred into 0.5ml polypropylene micro tubes and stored at -80C until shipment for metabolomic profiling.

Sample Preparation:

Sampleprep ID:SP002960
Sampleprep Summary:Following receipt, samples were inventoried and immediately stored and maintained at -80oC until processed. Each received sample was assigned a unique identifier, which was used to track all sample handling, tasks, and results. The samples and all derived aliquots were tracked throughout the process via an automated system. On the day of extraction, frozen samples were thawed on ice. Samples were prepared using the automated MicroLab STAR® system (Hamilton Company, Reno, NV). 100 µl of each sample was transferred into a well in a deepwell plate. Prior to extraction, several isotopically labelled standards were added to each sample to ensure accurate extraction of the samples. To remove proteins or dissociate small molecules bound to proteins or trapped in the precipitated protein matrix, proteins were precipitated with 500 µl of methanol under vigorous shaking for 2 minutes in a GenoGrinder 2000 (Glen Mills, Inc, Clifton, NJ) followed by centrifugation for 10 minutes at 680g.

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

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
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