Summary of Study ST001082

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 IDST001082
Study TitleCombined NMR and MS Analysis of PC patien serum (part-II)
Study SummarySerum of two groups of patients were analyzed using MS and NMR to find predictive markers of recurrence. Factor Sample Type in study design section refers to samples with Recurrence (R)/ No Recurrence (NR)/ Blank (B) / Pooled (P).
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 Date2020-01-13
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:SU001126
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
SA073015B_fBlank
SA073016sb_fBlank
SA073017MP1Blank
SA073018MP2Blank
SA073019MP5Blank
SA073020S19_2No Recurrence
SA073021S18_3No Recurrence
SA073022S19_3No Recurrence
SA073023S19_1No Recurrence
SA073024S20A_3No Recurrence
SA073025S18_2No Recurrence
SA073026S20A_2No Recurrence
SA073027S20A_1No Recurrence
SA073028S17_1No Recurrence
SA073029S16_2No Recurrence
SA073030S16_1No Recurrence
SA073031S16_3No Recurrence
SA073032S20B_1No Recurrence
SA073033S17_3No Recurrence
SA073034S17_2No Recurrence
SA073035S18_1No Recurrence
SA073036S21_2No Recurrence
SA073037S23_3No Recurrence
SA073038S23_2No Recurrence
SA073039S24_1No Recurrence
SA073040S24_2No Recurrence
SA073041S26_1No Recurrence
SA073042S24_3No Recurrence
SA073043S23_1No Recurrence
SA073044S22_3No Recurrence
SA073045S21_1No Recurrence
SA073046S20B_3No Recurrence
SA073047S14_3No Recurrence
SA073048S21_3No Recurrence
SA073049S22_2No Recurrence
SA073050S22_1No Recurrence
SA073051S20B_2No Recurrence
SA073052S13B_2No Recurrence
SA073053S6_2No Recurrence
SA073054S6_1No Recurrence
SA073055S6_3No Recurrence
SA073056S8_1No Recurrence
SA073057S8_3No Recurrence
SA073058S8_2No Recurrence
SA073059S5_3No Recurrence
SA073060S5_2No Recurrence
SA073061S3_3No Recurrence
SA073062S3_2No Recurrence
SA073063S4_1No Recurrence
SA073064S4_2No Recurrence
SA073065S5_1No Recurrence
SA073066S4_3No Recurrence
SA073067S9_1No Recurrence
SA073068S9_2No Recurrence
SA073069S13A_3No Recurrence
SA073070S13A_2No Recurrence
SA073071S13B_1No Recurrence
SA073072S26_2No Recurrence
SA073073S14_1No Recurrence
SA073074S13B_3No Recurrence
SA073075S13A_1No Recurrence
SA073076S12_3No Recurrence
SA073077S11_1No Recurrence
SA073078S9_3No Recurrence
SA073079S11_2No Recurrence
SA073080S11_3No Recurrence
SA073081S12_2No Recurrence
SA073082S12_1No Recurrence
SA073083S14_2No Recurrence
SA073084S27_2No Recurrence
SA073085S47_1No Recurrence
SA073086S46_3No Recurrence
SA073087S46_2No Recurrence
SA073088S47_2No Recurrence
SA073089S47_3No Recurrence
SA073090S66A_2No Recurrence
SA073091S66A_1No Recurrence
SA073092S46_1No Recurrence
SA073093S44_3No Recurrence
SA073094S43_1No Recurrence
SA073095S42_3No Recurrence
SA073096S43_2No Recurrence
SA073097S43_3No Recurrence
SA073098S44_2No Recurrence
SA073099S44_1No Recurrence
SA073100S66A_3No Recurrence
SA073101S66B_1No Recurrence
SA073102S72_2No Recurrence
SA073103S72_1No Recurrence
SA073104S72_3No Recurrence
SA073105S77_1No Recurrence
SA073106S77_3No Recurrence
SA073107S77_2No Recurrence
SA073108S70_3No Recurrence
SA073109S70_2No Recurrence
SA073110S66B_3No Recurrence
SA073111S66B_2No Recurrence
SA073112S67_1No Recurrence
SA073113S67_2No Recurrence
SA073114S70_1No Recurrence
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Collection:

Collection ID:CO001120
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:TR001140
Treatment Summary:These patients underwent prostatectomy after serum was collected.

Sample Preparation:

Sampleprep ID:SP001133
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 AN001766 AN001767
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters Xbridge BEH HILIC (75 x 2.1mm,2.5um) Waters Xbridge BEH HILIC (75 x 2.1mm,2.5um)
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:CH001248
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Xbridge BEH HILIC (75 x 2.1mm,2.5um)
Column Temperature:50
Flow Gradient:0-7.0 min. 63% A; 7.0-7.2 min 5% A with an increased flow rate of 500 µL min-1; 7.2-9.9 min 5% A with a decreased flow rate of 300 µL min-1; and 9.9-10.0 min held at 5% A
Flow Rate:300 µL min-1
Solvent A:5% acetonitrile/95% water; 10 mM ammonium formate; 0.05% ammonium hydroxide
Solvent B:100% acetonitrile; 0.05% ammonium hydroxide
Analytical Time:10 min
Chromatography Type:HILIC

MS:

MS ID:MS001633
Analysis ID:AN001766
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001634
Analysis ID:AN001767
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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