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 Date2023-03-07
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:SU002604
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
SA251745C003630
SA251746C003620
SA251747C006990
SA251748C006960
SA251749C003610
SA251750C006930
SA251751C003710
SA251752C003700
SA251753C003680
SA251754C003580
SA251755C003650
SA251756C007000
SA251757C003460
SA251758C003440
SA251759C007040
SA251760C007070
SA251761C003480
SA251762C003510
SA251763C007020
SA251764C003530
SA251765C003520
SA251766C003720
SA251767C003730
SA251768C003940
SA251769C006810
SA251770C006820
SA251771C003900
SA251772C006790
SA251773C006750
SA251774C006700
SA251775C006730
SA251776C003990
SA251777C003890
SA251778C006830
SA251779C003790
SA251780C006880
SA251781C003760
SA251782C003750
SA251783C003810
SA251784C003820
SA251785C003860
SA251786C003840
SA251787C006850
SA251788C003380
SA251789C003340
SA251790C007590
SA251791C002850
SA251792C002830
SA251793C002820
SA251794C007550
SA251795C007540
SA251796C002940
SA251797C002920
SA251798C002910
SA251799C002810
SA251800C002800
SA251801C002710
SA251802C002690
SA251803C002680
SA251804C002670
SA251805C002740
SA251806C007630
SA251807C002790
SA251808C002780
SA251809C002770
SA251810C007520
SA251811C002990
SA251812C003270
SA251813C007230
SA251814C003240
SA251815C007310
SA251816C003280
SA251817C003290
SA251818C003320
SA251819C007220
SA251820C003300
SA251821C003160
SA251822C007320
SA251823C003040
SA251824C007480
SA251825C007500
SA251826C003010
SA251827C003070
SA251828C003080
SA251829C003140
SA251830C003110
SA251831C003090
SA251832C004020
SA251833C004030
SA251834C005070
SA251835C005060
SA251836C006030
SA251837C006040
SA251838C005110
SA251839C005170
SA251840C005210
SA251841C005190
SA251842C005980
SA251843C005030
SA251844C005020
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Collection:

Collection ID:CO002597
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:TR002616
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:SP002610
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 AN004122 AN004123 AN004124 AN004125
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:CH003053
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:CH003054
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:CH003055
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:CH003056
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:MS003869
Analysis ID:AN004122
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments: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:MS003870
Analysis ID:AN004123
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments: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:MS003871
Analysis ID:AN004124
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments: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:MS003872
Analysis ID:AN004125
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments: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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