Summary of Study ST002420
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 PR001558. The data can be accessed directly via it's Project DOI: 10.21228/M89M65 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 | ST002420 |
Study Title | Colorectal cancer isobaric labeling for metabolite quantification |
Study Summary | A major challenge in reducing the death rate of colorectal cancer is to screen patients using low-invasive testing. Blood test shows a high compliance rate with reduced invasiveness. In this work, a multiplex isobaric tag labeling strategy coupled with mass spectrometry is adopted to relatively quantify primary and secondary amine-containing metabolites in serum for the discovery of metabolite biomarkers of colorectal cancer. Serum samples from patients at different risk statuses and colorectal cancer growth statuses are studied. Metabolite identification is based on accurate mass matching and/or retention time of labeled metabolite standards. We quantify 40 metabolites across all the serum samples, including 18 metabolites validated with standards. We find significantly decreased levels of threonine and asparagine in the patients with growing adenomas or high-risk adenomas (p < 0.05). Glutamine levels decrease in patients with adenomas of unknown growth status or high-risk adenomas. In contrast, arginine levels are elevated in patients with low-risk adenoma. Receiver operating characteristic analysis shows high sensitivity and specificity of these metabolites for detecting growing adenomas. Based on these results, we conclude that potential metabolite biomarkers identified here contribute to distinguishing colorectal patients with growing adenomas from normal individuals and patients with unknown growth status of adenomas. |
Institute | University of Wisconsin - Madison |
Last Name | Liu |
First Name | Yuan |
Address | 777 Highland ave, Madison, Wisconsin, 53705, USA |
liu788@wisc.edu | |
Phone | 6089606939 |
Submit Date | 2022-12-28 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2023-03-31 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
Analysis ID | AN003941 |
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Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Waters NanoAcquity |
Column | Waters ACQUITY UPLC BEH C18 (150 mm x 75 μm, 1.7 μm, 150 Å) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE |
Units | 1 |
Chromatography:
Chromatography ID: | CH002918 |
Chromatography Summary: | Four-plex pooled samples were reconstituted in 0.1% formic acid before injection. The HPLC-MS/MS analysis was conducted using a Waters nanoACQUITY UPLC coupled with Thermo Q Exactive Orbitrap MS. The separation column was in-house made with an emitter tip and dimensions of 75 μm inner diameter × 15 cm length. The column was packed with 1.7 μm, 150 Å, ethylene-bridged-hybrid (BEH) C18 material (Waters, Milford, MA). Mobile phase A was water containing 0.1% formic acid, and mobile phase B was acetonitrile containing 0.1% formic acid. The flow rate was set as 0.3 μL/min, and the LC gradient was 55 min and set as follows: 0−10 min, 3%-30% solvent B; 10−30 min, 30−80% B; 30-30.5 min, 80%-95% B; 30.5− 40.5 min, 95% B; 40.5−41 min, 95%-3% B; 41-55 min, 3% B. Positive ionization mode was used and full MS scans were acquired from m/z 180 to 800 at a resolution of 60 k, automatic gain control (AGC) was set as 5x 10^5, and a maximum injection time as set as 30 ms. The top 20 precursors were selected for normalized collision energy (NCE) dissociation (NCE = 30) with an isolation window of m/z 1, fixed first m/z 110, dynamic exclusion of 5 seconds, charge exclusion of >2, and a resolution of 35 k. |
Instrument Name: | Waters NanoAcquity |
Column Name: | Waters ACQUITY UPLC BEH C18 (150 mm x 75 μm, 1.7 μm, 150 Å) |
Column Temperature: | Room temperature |
Flow Gradient: | LC gradient was 55 min and set as follows: 0−10 min, 3%-30% solvent B; 10−30 min, 30−80% B; 30-30.5 min, 80%-95% B; 30.5− 40.5 min, 95% B; 40.5−41 min, 95%-3% B; 41-55 min, 3% B. |
Flow Rate: | 0.3 μL/min |
Solvent A: | 100% water; 0.01% formic acid |
Solvent B: | 100% acetonitrile; 0.01% formic acid |
Chromatography Type: | Reversed phase |