Summary of Study ST001054

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 PR000707. The data can be accessed directly via it's Project DOI: 10.21228/M8911D 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  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001054
Study TitleFingerprinting gastrointestinal diseases by 1H NMR
Study SummaryWe studied 64 patients admitted to the Florence main hospital emergency room with severe abdominal pain. A blood sample was drawn from each patient at admission, and the corresponding sera underwent 1H NMR metabolomics fingerprinting. Unsupervised PCA analysis showed a significant discrimination between a group of patients with symptoms of upper abdominal pain and a second group consisting of patients with diffuse abdominal/intestinal pain. Prompted by this observation, supervised statistical analysis (OPLS-DA) showed a very good discrimination (> 90 %) between the two groups of symptoms. Actually in the present study, upper abdominal pain may result from either symptomatic gallstones, cholecystitis or pancreatitis, while diffuse abdominal/intestinal pain may result from either intestinal ischemia, strangulated obstruction or mechanical obstruction. Although limited by the small number of samples from each of these six conditions, discrimination of these diseases was attempted. In the first symptom group, > 70% discrimination accuracy was obtained among symptomatic gallstones, pancreatitis and cholecystitis, while for the second symptom group > 85% classification accuracy was obtained for intestinal ischemia, strangulated obstruction and mechanical obstruction. No single metabolite stands up as a possible biomarker for any of these diseases, while the contribution of the whole 1H NMR serum fingerprint seems to be a promising candidate, to be confirmed on larger cohorts, as a first-line discriminator for these diseases.
Institute
Giotto Biotech s.r.l.
Last NameTakis
First NamePanteleimon
AddressVia Madonna del Piano 6
Emailtakis@giottobiotech.com
Phone+393423233750
Submit Date2018-09-15
Raw Data AvailableYes
Raw Data File Type(s)1r
Analysis Type DetailNMR
Release Date2018-09-27
Release Version1
Panteleimon Takis Panteleimon Takis
https://dx.doi.org/10.21228/M8911D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000707
Project DOI:doi: 10.21228/M8911D
Project Title:Fingerprinting gastrointestinal diseases by 1H NMR
Project Summary:A blood sample was drawn from each patient admitted to the Florence main hospital emergency room with severe abdominal pain. The corresponding sera underwent 1H NMR metabolomics fingerprinting to discriminate patients with symptoms of upper vs. diffuse abdominal/intestinal pain by the whole 1H NMR serum fingerprint and use it as a first-line discriminator for these symptoms and the diseases behind them.
Institute:Giotto Biotech s.r.l.
Last Name:Takis
First Name:Panteleimon
Address:Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
Email:takis@giottobiotech.com
Phone:+393423233750

Subject:

Subject ID:SU001096
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:50-90
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Abdominal pain location (symptom) clinical diagnosis
SA071486MAP003Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071487MAP291Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071488MAP280Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071489MAP121Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071490MAP117Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071491MAP088Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071492MAP306Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071493MAP271Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071494MAP036Diffuse abdominal/intestinal pain Intestinal Ischemia
SA071495MAP281Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071496MAP268Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071497MAP338Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071498MAP317Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071499MAP035Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071500MAP217Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071501MAP183Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071502MAP049Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071503MAP264Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071504MAP277Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071505MAP116Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071506MAP244Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071507MAP212Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071508MAP210Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071509MAP118Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071510MAP258Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071511MAP130Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071512MAP177Diffuse abdominal/intestinal pain Intestinal Mechanical Obstruction
SA071513MAP250Diffuse abdominal/intestinal pain Intestinal Strangulated Obstruction
SA071514MAP046Diffuse abdominal/intestinal pain Intestinal Strangulated Obstruction
SA071515MAP013Diffuse abdominal/intestinal pain Intestinal Strangulated Obstruction
SA071516MAP208Diffuse abdominal/intestinal pain Intestinal Strangulated Obstruction
SA071517MAP072Diffuse abdominal/intestinal pain Intestinal Strangulated Obstruction
SA071518MAP227Diffuse abdominal/intestinal pain Intestinal Strangulated Obstruction
SA071519MAP246Diffuse abdominal/intestinal pain Intestinal Strangulated Obstruction
SA071520MAP024Diffuse abdominal/intestinal pain Intestinal Strangulated Obstruction
SA071521MAP296Upper abdominal pain Cholecystitis
SA071522MAP209Upper abdominal pain Cholecystitis
SA071523MAP308Upper abdominal pain Cholecystitis
SA071524MAP315Upper abdominal pain Cholecystitis
SA071525MAP030Upper abdominal pain Cholecystitis
SA071526MAP152Upper abdominal pain Cholecystitis
SA071527MAP154Upper abdominal pain Cholecystitis
SA071528MAP044Upper abdominal pain Cholecystitis
SA071529MAP278Upper abdominal pain Cholecystitis
SA071530MAP031Upper abdominal pain Pancreatitis
SA071531MAP058Upper abdominal pain Pancreatitis
SA071532MAP101Upper abdominal pain Pancreatitis
SA071533MAP331Upper abdominal pain Pancreatitis
SA071534MAP295Upper abdominal pain Pancreatitis
SA071535MAP311Upper abdominal pain Pancreatitis
SA071536MAP230Upper abdominal pain Pancreatitis
SA071537MAP066Upper abdominal pain Pancreatitis
SA071538MAP158Upper abdominal pain Symptomatic Gallstones
SA071539MAP119Upper abdominal pain Symptomatic Gallstones
SA071540MAP222Upper abdominal pain Symptomatic Gallstones
SA071541MAP011Upper abdominal pain Symptomatic Gallstones
SA071542MAP171Upper abdominal pain Symptomatic Gallstones
SA071543MAP111Upper abdominal pain Symptomatic Gallstones
SA071544MAP228Upper abdominal pain Symptomatic Gallstones
SA071545MAP239Upper abdominal pain Symptomatic Gallstones
SA071546MAP329Upper abdominal pain Symptomatic Gallstones
SA071547MAP232Upper abdominal pain Symptomatic Gallstones
SA071548MAP005Upper abdominal pain Symptomatic Gallstones
SA071549MAP050Upper abdominal pain Symptomatic Gallstones
Showing results 1 to 64 of 64

Collection:

Collection ID:CO001090
Collection Summary:Blood was drawn at admission to the emergency room, after acquiring the appropriate informed consent (explaining to the patients the aims of the study and ensuring them the complete anonymity of the data collected). Each sample consisted of 8-10 cc of peripheral blood and was immediately ultra-centrifuged for about 10-15 minutes at 1300 RCF. Serum samples were then subdivided in small aliquots (about 500-600 microliters each), and immediately stored at -80 °C.
Collection Protocol Filename:Blood_collection.docx
Sample Type:Blood (serum)
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001110
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP001103
Sampleprep Summary:Frozen serum samples were thawed at room temperature and 300 μl of each sample were added to a total of 300 μl of a sodium phosphate buffer at pH 7.4 (75 mM Na2HPO4, 20 % (v/v) D2O, 0.025 % (v/v) NaN3 and 0.8 % (w/v) sodium trimethylsilyl[2,2,3,3-22H4]propionate (TMSP)). From the mixture, 450 μl were transferred into a 4.25 mm NMR disposable tube, acquired from Bruker BioSpin srl.
Sampleprep Protocol Filename:NMR_Sample_preparation.docx
Processing Storage Conditions:Room temperature

Analysis:

Analysis ID:AN001723
Analysis Type:NMR
Analysis Protocol File:NMR_details.docx
Data Format:1r
Num Factors:6

NMR:

NMR ID:NM000129
Analysis ID:AN001723
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Spectrometer Frequency:600 MHz
NMR Solvent:Serum D2O Buffer
NMR Tube Size:4.25 mm
Temperature:36.85
Number Of Scans:64
Dummy Scans:4
Acquisition Time:2.7
Relaxation Delay:4
Line Broadening:1 Hz
Chemical Shift Ref Std:TMSP at 0 ppm
Binned Increment:0.02
Binned Data Excluded Range:4.40-5.00 (ppm) H2O region
  logo