Summary of study ST000918

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 PR000634. The data can be accessed directly via it's Project DOI: 10.21228/M8QM3R 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 IDST000918
Study TitlePlasma metabolic fingerprint for breast cancer (MS) - part I
Study Typecontrol - case
Study SummaryBreast cancer is a highly heterogeneous disease associated with metabolic reprogramming. The shifts in the metabolome caused by breast cancer still lack data from Latin populations of Hispanic origin. In this pilot study, metabolomic and lipidomic approaches were performed to establish a plasma metabolic fingerprint of Colombian Hispanic women with breast cancer. NMR, GC-MS and LC-MS datasets were combined and compared. Statistics showed discrimination between breast cancer and healthy subjects on all analytical platforms.
Institute
Universidad de los Andes, Colombia
DepartmentChemistry
Last NameCala
First NameMonica
AddressCra. 1 #18a-12
Emailmp.cala10@uniandes.edu.co
Phone+571 3394949
Submit Date2017-12-29
Num Groups2
Total Subjects58
Analysis Type DetailGC/LC-MS
Release Date2018-02-07
Release Version1
Monica Cala Monica Cala
https://dx.doi.org/10.21228/M8QM3R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000634
Project DOI:doi: 10.21228/M8QM3R
Project Title:Multiplatform plasma metabolic and lipid fingerprinting of breast cancer: a pilot control-case study in Colombian Hispanic women.
Project Summary:In this pilot study, a metabolomic approaches was performed to establish a plasma metabolic fingerprint of Colombian Hispanic women with breast cancer. Data from NMR, GC-MS and LC-MS were combined and compared.
Institute:Universidad de los Andes, Colombia
Department:Chemistry
Last Name:Cala
First Name:Monica
Address:Cra. 1 #18a-12
Email:mp.cala10@uniandes.edu.co
Phone:+571 3394949

Subject:

Subject ID:SU000956
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:35 - 65
Weight Or Weight Range:61 - 75
Gender:Female

Factors:

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

mb_sample_id local_sample_id Disease Status
SA054066BCP21Breast cancer patient
SA054067BCP23Breast cancer patient
SA054068BCP20Breast cancer patient
SA054069BCP18Breast cancer patient
SA054070BCP17Breast cancer patient
SA054071BCP24Breast cancer patient
SA054072BCP19Breast cancer patient
SA054073BCP25Breast cancer patient
SA054074BCP29Breast cancer patient
SA054075BCP01Breast cancer patient
SA054076BCP28Breast cancer patient
SA054077BCP27Breast cancer patient
SA054078BCP26Breast cancer patient
SA054079BCP16Breast cancer patient
SA054080BCP22Breast cancer patient
SA054081BCP06Breast cancer patient
SA054082BCP07Breast cancer patient
SA054083BCP05Breast cancer patient
SA054084BCP04Breast cancer patient
SA054085BCP02Breast cancer patient
SA054086BCP15Breast cancer patient
SA054087BCP08Breast cancer patient
SA054088BCP03Breast cancer patient
SA054089BCP13Breast cancer patient
SA054090BCP09Breast cancer patient
SA054091BCP12Breast cancer patient
SA054092BCP14Breast cancer patient
SA054093BCP10Breast cancer patient
SA054094BCP11Breast cancer patient
SA054095CP20Control patient
SA054096CP21Control patient
SA054097CP22Control patient
SA054098CP19Control patient
SA054099CP17Control patient
SA054100CP23Control patient
SA054101CP18Control patient
SA054102CP27Control patient
SA054103CP29Control patient
SA054104CP16Control patient
SA054105CP28Control patient
SA054106CP26Control patient
SA054107CP25Control patient
SA054108CP24Control patient
SA054109CP01Control patient
SA054110CP06Control patient
SA054111CP07Control patient
SA054112CP05Control patient
SA054113CP04Control patient
SA054114CP02Control patient
SA054115CP03Control patient
SA054116CP08Control patient
SA054117CP09Control patient
SA054118CP13Control patient
SA054119CP14Control patient
SA054120CP12Control patient
SA054121CP11Control patient
SA054122CP10Control patient
SA054123CP15Control patient
Showing results 1 to 58 of 58

Collection:

Collection ID:CO000950
Collection Summary:Venous blood samples were taken in the morning after overnight fasting and were collected using K3EDTA tubes
Sample Type:Blood
Collection Method:Venous
Collection Frequency:one
Volumeoramount Collected:5 mL
Storage Conditions:-80C
Additives:K3EDTA
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000970
Treatment Summary:None
Human Fasting:Overnight

Sample Preparation:

Sampleprep ID:SP000963
Sampleprep Summary:40 µL of plasma was deproteinized with cold acetonitrile (1:3,−20 °C), followed by a two-step derivatization: (i) methoximation with O-Methoxyamine hydrochloride in pyridine (15 mg/mL, room temperature, 16 h) followed by (ii) silylation with BSTFA containing 1% TMCS (70 °C, 1 h).
Processing Method:Protein precipitation followed by metabolite extraction
Processing Storage Conditions:On ice
Extraction Method:Acetonitrile
Sample Derivatization:Methoximation and silylation

Combined analysis:

Analysis ID AN001503 AN001504 AN001505
Analysis type MS MS MS
Chromatography type GC Normal phase Normal phase
Chromatography system Agilent Agilent 1200 Agilent 1200
Column Zebron ZB-5MSi capillary GC column Phenomenex Kinetex C18 (150 x 2.1mm, 2.6 um) Phenomenex Kinetex C18 (150 x 2.1mm, 2.6 um)
MS Type EI ESI ESI
MS instrument type Single quadrupole QTOF QTOF
MS instrument name Agilent 5973 Agilent 6530 QTOF Agilent 6530 QTOF
Ion Mode POSITIVE POSITIVE NEGATIVE
Units peak area peak area peak area

Chromatography:

Chromatography ID:CH001060
Chromatography Summary:Untargeted GC/MS method
Instrument Name:Agilent
Column Name:Zebron ZB-5MSi capillary GC column
Column Temperature:0-1 min 60ªC 1-33 min to 320ªC
Flow Rate:1.0 mL/min
Sample Injection:2 uL
Chromatography Type:GC
  
Chromatography ID:CH001061
Chromatography Summary:Untargeted LC/MS method
Chromatography Comments:HPLC system 1200 series coupled to Q-TOF 6520
Instrument Name:Agilent 1200
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm, 2.6 um)
Column Pressure:300 bar
Column Temperature:40°C
Flow Gradient:25% B increased then to 95% B in 35 min, returned to initial conditions in 1 min and was kept constant for 9 min to ensure re-equilibration of the column
Flow Rate:0.3 mL/min
Sample Injection:10 uL
Solvent A:0.1% (v/v) formic acid in water
Solvent B:0.1% (v/v) formic acid in acetonitrile
Chromatography Type:Normal phase

MS:

MS ID:MS001386
Analysis ID:AN001503
Instrument Name:Agilent 5973
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
Helium Flow:1.0 mL/min
Ion Source Temperature:150 C
Ionization:Electron ionization
Ionization Energy:70 eV
Source Temperature:230 ºC
Scan Range Moverz:50 - 600
Scanning:1.38 scan/s
  
MS ID:MS001387
Analysis ID:AN001504
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3500 V
Scan Range Moverz:100 / 1200 m/z
Scanning:1.38 scan/s
  
MS ID:MS001388
Analysis ID:AN001505
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:4000 V
Scan Range Moverz:100 / 1200 m/z
Scanning:1.38 scan/s
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