Summary of Study ST000590

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 PR000431. The data can be accessed directly via it's Project DOI: 10.21228/M8BK5R 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.

Show all samples  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files
Study IDST000590
Study TitleHuman Plasma Metabolomics in Age-related Macular Degeneration (AMD) Using Nuclear Magnetic Resonance Spectroscopy
Study TypeObservational, cross-sectional, multi-site study, NMR metabolomics
Study SummaryMulti-site, cross-sectional study, including subjects with Age-related Macular Degeneration (early, intermediate and late disease) and a control group of subjects without any macular diseases. Plasma metabolomic profiles were assessed using Nuclear Magnetic Resonance Spectroscopy (NMR). Multivariate statistics were performed to compare metabolomic profiles of AMD patients vs controls.
Institute
University of Aveiro
DepartmentDepartment of Chemistry and CICECO_Aveiro Institute of Materials
LaboratoryUniversity of Aveiro
Last NameGil
First NameAna
AddressCampus de Santiago, Aveiro, Aveiro, 3810-193, Portugal
Emailagil@ua.pt
Phone+351234370707
Submit Date2017-02-20
Num Groups4
Total Subjects396
Num Males143
Num Females253
Analysis Type DetailNMR
Release Date2017-07-10
Release Version1
Ana Gil Ana Gil
https://dx.doi.org/10.21228/M8BK5R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000431
Project DOI:doi: 10.21228/M8BK5R
Project Title:Age-related Macular Degeneration: A Novel Integrative Approach to Identify Biomarkers
Project Type:Cross-sectional, observational, multi-site, metabolomics by NMR
Project Summary:This is a collaborative project between several Portuguese Institutions and Massachusetts Eye and Ear, Harvard Medical School, Boston, US. The main goal is to identify integrative biomarkers of Age-related Macular Degeneration (AMD). We prospectively recruited subjects in both countries. For all participants, a complete medical history was obtained, and they were all submitted to a complete ophthalmologic exam, as well as imaging. All subjects provided fasting blood and urine samples.
Institute:University of Aveiro
Department:Department of Chemistry, CICECO-Aveiro Institute of Materials
Laboratory:University of Aveiro
Last Name:Gil
First Name:Ana
Address:Campus de Santiago, Aveiro, Aveiro, 3810-193, Portugal
Email:agil@ua.pt
Phone:+351234370707

Subject:

Subject ID:SU000613
Subject Type:HUman
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:51-95
Gender:253 female; 143 male
Human Smoking Status:5 smokers; 113 ex-smokers; 275 non smokers
Human Inclusion Criteria:For AMD group: clinical diagnosis of AMD, confirmed on color fundus photographs; For controls: age equal or superior than 50 years old, with normal macular health
Human Exclusion Criteria:Diagnosis of any other vitreoretinal disease, active uveitis or ocular infection, significant media opacities that precluded the observation of the ocular fundus, refractive error equal or greater than 6 diopters of spherical equivalent, past history of retinal surgery, history of any ocular surgery or intra-ocular procedure (such as laser and intra-ocular injections) within the 90 days prior to enrolment, and diagnosis of diabetes mellitus, with or without concomitant diabetic retinopathy.
Species Group:Human

Factors:

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

mb_sample_id local_sample_id AMD stage Gender Smoking Cohort
SA032195AMD03_050Control Female Ex smoker Boston
SA032196AMD03_009Control Female Ex smoker Boston
SA032197AMD03_022Control Female Ex smoker Boston
SA032198AMD03_074Control Female Ex smoker Boston
SA032199AMD03_084Control Female Ex smoker Boston
SA032200AMD03_082Control Female Ex smoker Boston
SA032201AMD03_001Control Female Ex smoker Boston
SA032202AMD03_039Control Female Ex smoker Boston
SA032203AMD03_085Control Female Non smoker Boston
SA032204AMD03_017Control Female Non smoker Boston
SA032205AMD03_025Control Female Non smoker Boston
SA032206AMD03_087Control Female Non smoker Boston
SA032207AMD03_005Control Female Non smoker Boston
SA032208AMD03_094Control Female Non smoker Boston
SA032209AMD03_090Control Female Non smoker Boston
SA032210AMD03_029Control Female Non smoker Boston
SA032211AMD03_003Control Female Non smoker Boston
SA032212AMD03_055Control Female Non smoker Boston
SA032213AMD03_037Control Female Non smoker Boston
SA032214AMD03_046Control Female Non smoker Boston
SA032215AMD03_059Control Female Non smoker Boston
SA032216AMD03_042Control Female Non smoker Boston
SA032217AMD05_038Control Female Non smoker Coimbra
SA032218AMD05_036Control Female Non smoker Coimbra
SA032219AMD05_043Control Female Non smoker Coimbra
SA032220AMD05_044Control Female Non smoker Coimbra
SA032221AMD05_047Control Female Non smoker Coimbra
SA032222AMD05_046Control Female Non smoker Coimbra
SA032223AMD05_035Control Female Non smoker Coimbra
SA032224AMD05_032Control Female Non smoker Coimbra
SA032225AMD05_015Control Female Non smoker Coimbra
SA032226AMD05_048Control Female Non smoker Coimbra
SA032227AMD05_023Control Female Non smoker Coimbra
SA032228AMD05_085Control Female Non smoker Coimbra
SA032229AMD05_091Control Female Non smoker Coimbra
SA032230AMD05_031Control Female Non smoker Coimbra
SA032231AMD05_034Control Female Non smoker Coimbra
SA032232AMD05_029Control Female Non smoker Coimbra
SA032233AMD05_072Control Female Non smoker Coimbra
SA032234AMD05_059Control Female Non smoker Coimbra
SA032235AMD05_069Control Female Non smoker Coimbra
SA032236AMD05_083Control Female Non smoker Coimbra
SA032237AMD05_061Control Female Non smoker Coimbra
SA032238AMD05_064Control Female Non smoker Coimbra
SA032239AMD05_058Control Female Non smoker Coimbra
SA032240AMD05_076Control Female Non smoker Coimbra
SA032241AMD05_073Control Female Non smoker Coimbra
SA032242AMD05_074Control Female Non smoker Coimbra
SA032243AMD03_073Control Female Smoker Boston
SA032244AMD03_007Control Female Smoker Boston
SA032245AMD03_013Control Male Ex smoker Boston
SA032246AMD03_011Control Male Ex smoker Boston
SA032247AMD03_067Control Male Ex smoker Boston
SA032248AMD03_093Control Male Ex smoker Boston
SA032249AMD03_088Control Male Ex smoker Boston
SA032250AMD03_032Control Male Ex smoker Boston
SA032251AMD03_068Control Male Ex smoker Boston
SA032252AMD03_053Control Male Ex smoker Boston
SA032253AMD05_080Control Male Ex smoker Coimbra
SA032254AMD05_082Control Male Ex smoker Coimbra
SA032255AMD05_013Control Male Ex smoker Coimbra
SA032256AMD05_084Control Male Ex smoker Coimbra
SA032257AMD05_053Control Male Ex smoker Coimbra
SA032258AMD05_068Control Male Ex smoker Coimbra
SA032259AMD05_081Control Male Ex smoker Coimbra
SA032260AMD04_006Control Male Ex smoker Coimbra
SA032261AMD03_075Control Male Non smoker Boston
SA032262AMD03_021Control Male Non smoker Boston
SA032263AMD03_077Control Male Non smoker Boston
SA032264AMD03_038Control Male Non smoker Boston
SA032265AMD03_043Control Male Non smoker Boston
SA032266AMD03_002Control Male Non smoker Boston
SA032267AMD03_052Control Male Non smoker Boston
SA032268AMD03_028Control Male Non smoker Boston
SA032269AMD05_030Control Male Non smoker Coimbra
SA032270AMD05_003Control Male Non smoker Coimbra
SA032271AMD05_049Control Male Non smoker Coimbra
SA032272AMD05_005Control Male Non smoker Coimbra
SA032273AMD05_037Control Male Non smoker Coimbra
SA032274AMD05_051Control Male Non smoker Coimbra
SA032275AMD05_033Control Male Non smoker Coimbra
SA032276AMD05_065Control Male Non smoker Coimbra
SA032277AMD03_012Early Female Ex smoker Boston
SA032278AMD02_039Early Female Ex smoker Boston
SA032279AMD01_048Early Female Ex smoker Boston
SA032280AMD03_092Early Female Ex smoker Boston
SA032281AMD03_051Early Female Ex smoker Boston
SA032282AMD03_078Early Female Ex smoker Boston
SA032283AMD03_047Early Female Non smoker Boston
SA032284AMD03_070Early Female Non smoker Boston
SA032285AMD03_040Early Female Non smoker Boston
SA032286AMD03_072Early Female Non smoker Boston
SA032287AMD03_026Early Female Non smoker Boston
SA032288AMD03_019Early Female Non smoker Boston
SA032289AMD03_023Early Female Non smoker Boston
SA032290AMD03_018Early Female Non smoker Boston
SA032291AMD02_038Early Female Non smoker Boston
SA032292AMD03_004Early Female Non smoker Boston
SA032293AMD03_006Early Female Non smoker Boston
SA032294AMD01_080Early Female Non smoker Boston
Showing page 1 of 4     Results:    1  2  3  4  Next     Showing results 1 to 100 of 396

Collection:

Collection ID:CO000607
Collection Summary:For all participants, fasting blood samples were collected into sodium-heparin tubes, and centrifuged within 30 min (1500 rpm, 10 min, 20ºC). Plasma aliquots of 1.5 mL (MEE) and 5 mL (FMUC/AIBILI) were transferred into sterile cryovials and stored at -80ºC. Plasma samples from MEE were shipped to Portugal for metabolomic profiling in dry ice (through TNT Express, USA, INC). Samples arrived frozen in less than 48 hours and were immediately stored at -80ºC until NMR analysis.
Sample Type:Blood plasma
Collection Method:For all participants, fasting blood samples were collected into sodium-heparin tubes, and centrifuged within 30 min (1500 rpm, 10 min, 20ºC). Plasma aliquots of 1.5 mL (MEE) and 5 mL (FMUC/AIBILI) were transferred into sterile cryovials and stored at -80ºC. Plasma samples from MEE were shipped to Portugal for metabolomic profiling in dry ice (through TNT Express, USA, INC). Samples arrived frozen in less than 48 hours and were immediately stored at -80ºC until NMR analysis.
Collection Location:Retina Service, Massachusetts Eye and Ear, Harvard Medical School, Boston, US; Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Association for Innovation and Biomedical Research on Light and Image (AIBILI), Coimbra, Portugal.
Collection Frequency:one collection
Volumeoramount Collected:9 tp 10 mL
Storage Conditions:Plasma aliquots were stored at -80ºC. Plasma samples from MEE were shipped to Portugal for metabolomic profiling in dry ice (through TNT Express, USA, INC). Samples arrived frozen in less than 48 hours and were immediately stored at -80ºC until NMR analysis.
Collection Vials:sodium-heparin tubes
Storage Vials:sterile cryovials
Collection Tube Temp:room temperature
Additives:No
Blood Serum Or Plasma:Yes, blood samples were collected, which were then centrifuged to obtain plasma

Treatment:

Treatment ID:TR000627
Treatment Summary:No treatments were applied in the context of this project

Sample Preparation:

Sampleprep ID:SP000620
Sampleprep Summary:Prior to analysis, plasma samples were thawed at room temperature and homogenized in a vortex mixer. Then, 400 µl of saline solution (NaCl 0.9% in 10% D2O) were added to 200 µl of sample. After centrifugation (4500 g, 5min, 25ºC), 550 µl of each sample was transferred to a 5 mm NMR tube.

Analysis:

Analysis ID:AN000905
Laboratory Name:University of Aveiro
Analysis Type:NMR
Acquisition Date:From June 2015 to September 2017
Software Version:Topsoin 3.2
Operator Name:Daniela Duarte and Ana Sofia Martins
Data Format:NMR spectra converted into excel
Num Factors:33

NMR:

NMR ID:NM000102
Analysis ID:AN000905
Instrument Name:Bruker Avance DRX 500 spectrometer
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Spectrometer Frequency:500 MHz
NMR Probe:TXI
NMR Solvent:H2O+D2O (10%)_salt
NMR Tube Size:5 mm
Shimming Method:Automated
Pulse Sequence:cpmgpr1d and ledbpgp2s1dpr
Water Suppression:Yes
Pulse Width:7 us
Receiver Gain:128 and 203
Chemical Shift Ref Cpd:glucose
Temperature:300 K
Number Of Scans:256 and 128
Dummy Scans:4
Acquisition Time:1.59 s
Relaxation Delay:4 s
Spectral Width:20,6557 Hz
Num Data Points Acquired:32 k
Real Data Points:32 k
Line Broadening:0,3 Hz
Zero Filling:64 k
Baseline Correction Method:manual
Chemical Shift Ref Std:glucose (5.23 ppm)
Binned Increment:full resolution
Binned Data Excluded Range:4.50-5.15 ppm
  logo