Summary of Study ST001081

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 PR000724. The data can be accessed directly via it's Project DOI: 10.21228/M83D5V 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 IDST001081
Study TitleCombined NMR and MS Analysis of PC patient serum (part-I)
Study SummarySerum of two groups of patients were analyzed using MS and NMR to find predictive markers of recurrence
Institute
Georgia Institute of Technology
DepartmentDepartment of Chemistry
LaboratoryFernandez
Last NameFernandez
First NameFacundo
Address901 Atlantic Dr NE, Atlanta, GA, 30332, USA
Emailfernandez@gatech.edu
Phone404-385-4432
Submit Date2018-10-19
Num Groups2
Total Subjects80
Num Males80
Analysis Type DetailLC-MS
Release Date2019-10-11
Release Version1
Facundo Fernandez Facundo Fernandez
https://dx.doi.org/10.21228/M83D5V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000724
Project DOI:doi: 10.21228/M83D5V
Project Title:Preoperative Metabolic Signatures of Prostate Cancer Recurrence Following Radical Prostatectomy
Project Summary:Prostate cancer patient serum was analyzed using HILIC and RP LC/MS and NMR.
Institute:Georgia Institute of Technology
Last Name:Fernandez
First Name:Facundo
Address:901 Atlantic Dr NE, Atlanta, GA, 30332, USA
Email:fernandez@gatech.edu
Phone:404-385-4432

Subject:

Subject ID:SU001125
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:44-70
Gender:Male
Human Inclusion Criteria:Prostatectomy patients

Factors:

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

mb_sample_id local_sample_id Sample Type
SA072847b1_2Blank
SA072848b3Blank
SA072849sb1Blank
SA072850sb_fBlank
SA072851S19_1No Recurrence
SA072852S18_2No Recurrence
SA072853S20_1No Recurrence
SA072854S18_1No Recurrence
SA072855S19_2No Recurrence
SA072856S16_2No Recurrence
SA072857S16_1No Recurrence
SA072858S20_2No Recurrence
SA072859S17_1No Recurrence
SA072860S17_2No Recurrence
SA072861S22_1No Recurrence
SA072862S24_1No Recurrence
SA072863S24_2No Recurrence
SA072864S26_1No Recurrence
SA072865S23_2No Recurrence
SA072866S23_1No Recurrence
SA072867S21_2No Recurrence
SA072868S14_2No Recurrence
SA072869S22_2No Recurrence
SA072870S21_1No Recurrence
SA072871S13_1No Recurrence
SA072872S6_2No Recurrence
SA072873S7_1No Recurrence
SA072874S7_2No Recurrence
SA072875S6_1No Recurrence
SA072876S5_2No Recurrence
SA072877S4_1No Recurrence
SA072878S4_2No Recurrence
SA072879S5_1No Recurrence
SA072880S8_1No Recurrence
SA072881S8_2No Recurrence
SA072882S12_2No Recurrence
SA072883S26_2No Recurrence
SA072884S13_2No Recurrence
SA072885S12_1No Recurrence
SA072886S11_2No Recurrence
SA072887S9_1No Recurrence
SA072888S9_2No Recurrence
SA072889S11_1No Recurrence
SA072890S14_1No Recurrence
SA072891S28_1No Recurrence
SA072892S46_1No Recurrence
SA072893S46_2No Recurrence
SA072894S47_1No Recurrence
SA072895S47_2No Recurrence
SA072896S44_2No Recurrence
SA072897S44_1No Recurrence
SA072898S42_2No Recurrence
SA072899S43_1No Recurrence
SA072900S43_2No Recurrence
SA072901S66_1No Recurrence
SA072902S66_2No Recurrence
SA072903S72_2No Recurrence
SA072904S77_1No Recurrence
SA072905S77_2No Recurrence
SA072906S72_1No Recurrence
SA072907S70_2No Recurrence
SA072908S67_1No Recurrence
SA072909S67_2No Recurrence
SA072910S70_1No Recurrence
SA072911S42_1No Recurrence
SA072912S41_2No Recurrence
SA072913S30_1No Recurrence
SA072914S30_2No Recurrence
SA072915S31_1No Recurrence
SA072916S29_2No Recurrence
SA072917S29_1No Recurrence
SA072918S27_2No Recurrence
SA072919S3_2No Recurrence
SA072920S28_2No Recurrence
SA072921S31_2No Recurrence
SA072922S32_1No Recurrence
SA072923S38_1No Recurrence
SA072924S38_2No Recurrence
SA072925S41_1No Recurrence
SA072926S36_2No Recurrence
SA072927S36_1No Recurrence
SA072928S32_2No Recurrence
SA072929S33_1No Recurrence
SA072930S33_2No Recurrence
SA072931S27_1No Recurrence
SA072932S2_1No Recurrence
SA072933S3_1No Recurrence
SA072934S1_1No Recurrence
SA072935S1_2No Recurrence
SA072936S2_2No Recurrence
SA072937P2Pooled
SA072938P2_2Pooled
SA072939P1_2Pooled
SA072940P1Pooled
SA072941S51_1Recurrence
SA072942S51_2Recurrence
SA072943S52_1Recurrence
SA072944S50_2Recurrence
SA072945S50_1Recurrence
SA072946S49_2Recurrence
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Collection:

Collection ID:CO001119
Collection Summary:After Emory Institutional Review Board (IRB) approval, patients were consented and blood collected in SST Serum Separation Tubes: Hemogard (Fisher Scientific). Serum was separated by centrifugation at 1300 rcf for 20 min at 4 °C. Serum aliquots were stored long term in liquid nitrogen until removed for analysis.
Sample Type:Blood (serum)
Collection Location:Emory University
Collection Frequency:Pre-operative
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001139
Treatment Summary:These patients underwent prostatectomy after serum was collected.

Sample Preparation:

Sampleprep ID:SP001132
Sampleprep Summary:Proteins were precipitated from serum samples using either MeOH (for HILIC LC/MS and NMR) or Isopropanol (for RP LC/MS). Samples stored in -80 until analyzed
Extract Storage:-80C

Combined analysis:

Analysis ID AN001764 AN001765
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters Acquity BEH C18 (50 x 2.1mm,1.7um) Waters Acquity BEH C18 (50 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Relative abundance Relative abundance

Chromatography:

Chromatography ID:CH001247
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Acquity BEH C18 (50 x 2.1mm,1.7um)
Column Temperature:40
Flow Gradient:0-1 min 55% A: 1-1.1 min. 50% A; 1.1-5.0 min 45% A; 5.0-5.1 min 30% A; 5.1-8.0 min 1%A; 8.0-8.1 min 60% A; and 8.1-9.5 min held at 60% A
Flow Rate:400 µL min-1
Solvent A:40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:10% acetonitrile/90% isopropanol; 0.1% formic acid; 10 mM ammonium formate
Analytical Time:9.5 min
Chromatography Type:Reversed phase

MS:

MS ID:MS001631
Analysis ID:AN001764
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001632
Analysis ID:AN001765
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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