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.
Study ID | ST001054 |
Study Title | Fingerprinting gastrointestinal diseases by 1H NMR |
Study Summary | We 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 Name | Takis |
First Name | Panteleimon |
Address | Via Madonna del Piano 6 |
takis@giottobiotech.com | |
Phone | +393423233750 |
Submit Date | 2018-09-15 |
Raw Data Available | Yes |
Raw Data File Type(s) | 1r |
Analysis Type Detail | NMR |
Release Date | 2018-09-27 |
Release Version | 1 |
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 |
Species Group: | Mammals |
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 |
---|---|---|---|
SA071486 | MAP003 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071487 | MAP291 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071488 | MAP280 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071489 | MAP121 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071490 | MAP117 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071491 | MAP088 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071492 | MAP306 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071493 | MAP271 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071494 | MAP036 | Diffuse abdominal/intestinal pain | Intestinal Ischemia |
SA071495 | MAP281 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071496 | MAP268 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071497 | MAP338 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071498 | MAP317 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071499 | MAP035 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071500 | MAP217 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071501 | MAP183 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071502 | MAP049 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071503 | MAP264 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071504 | MAP277 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071505 | MAP116 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071506 | MAP244 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071507 | MAP212 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071508 | MAP210 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071509 | MAP118 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071510 | MAP258 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071511 | MAP130 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071512 | MAP177 | Diffuse abdominal/intestinal pain | Intestinal Mechanical Obstruction |
SA071513 | MAP250 | Diffuse abdominal/intestinal pain | Intestinal Strangulated Obstruction |
SA071514 | MAP046 | Diffuse abdominal/intestinal pain | Intestinal Strangulated Obstruction |
SA071515 | MAP013 | Diffuse abdominal/intestinal pain | Intestinal Strangulated Obstruction |
SA071516 | MAP208 | Diffuse abdominal/intestinal pain | Intestinal Strangulated Obstruction |
SA071517 | MAP072 | Diffuse abdominal/intestinal pain | Intestinal Strangulated Obstruction |
SA071518 | MAP227 | Diffuse abdominal/intestinal pain | Intestinal Strangulated Obstruction |
SA071519 | MAP246 | Diffuse abdominal/intestinal pain | Intestinal Strangulated Obstruction |
SA071520 | MAP024 | Diffuse abdominal/intestinal pain | Intestinal Strangulated Obstruction |
SA071521 | MAP296 | Upper abdominal pain | Cholecystitis |
SA071522 | MAP209 | Upper abdominal pain | Cholecystitis |
SA071523 | MAP308 | Upper abdominal pain | Cholecystitis |
SA071524 | MAP315 | Upper abdominal pain | Cholecystitis |
SA071525 | MAP030 | Upper abdominal pain | Cholecystitis |
SA071526 | MAP152 | Upper abdominal pain | Cholecystitis |
SA071527 | MAP154 | Upper abdominal pain | Cholecystitis |
SA071528 | MAP044 | Upper abdominal pain | Cholecystitis |
SA071529 | MAP278 | Upper abdominal pain | Cholecystitis |
SA071530 | MAP031 | Upper abdominal pain | Pancreatitis |
SA071531 | MAP058 | Upper abdominal pain | Pancreatitis |
SA071532 | MAP101 | Upper abdominal pain | Pancreatitis |
SA071533 | MAP331 | Upper abdominal pain | Pancreatitis |
SA071534 | MAP295 | Upper abdominal pain | Pancreatitis |
SA071535 | MAP311 | Upper abdominal pain | Pancreatitis |
SA071536 | MAP230 | Upper abdominal pain | Pancreatitis |
SA071537 | MAP066 | Upper abdominal pain | Pancreatitis |
SA071538 | MAP158 | Upper abdominal pain | Symptomatic Gallstones |
SA071539 | MAP119 | Upper abdominal pain | Symptomatic Gallstones |
SA071540 | MAP222 | Upper abdominal pain | Symptomatic Gallstones |
SA071541 | MAP011 | Upper abdominal pain | Symptomatic Gallstones |
SA071542 | MAP171 | Upper abdominal pain | Symptomatic Gallstones |
SA071543 | MAP111 | Upper abdominal pain | Symptomatic Gallstones |
SA071544 | MAP228 | Upper abdominal pain | Symptomatic Gallstones |
SA071545 | MAP239 | Upper abdominal pain | Symptomatic Gallstones |
SA071546 | MAP329 | Upper abdominal pain | Symptomatic Gallstones |
SA071547 | MAP232 | Upper abdominal pain | Symptomatic Gallstones |
SA071548 | MAP005 | Upper abdominal pain | Symptomatic Gallstones |
SA071549 | MAP050 | Upper 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 |