Summary of Study ST003027
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 PR001876. The data can be accessed directly via it's Project DOI: 10.21228/M87426 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 | ST003027 |
| Study Title | NMR- and MS-based omics reveal characteristic metabolome atlas and optimize biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma (part-Ⅳ) |
| Study Summary | Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. We conducted NMR- and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- and one-week post-operative sera and urines from 560 participants across three hospitals, with machine learning, logistic regression and WGCNA. Aberrations in 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout the ESCC evolution, and were reflected in 16 serum and 10 urine metabolic signatures that were consistently identified by NMR and MS in both discovery and validation sets. NMR-based simplified panels of any five serum or urine metabolites outperformed clinical serological tumor markers (AUC = 0.984 and 0.930, respectively), and were effective in distinguishing early-stage ESCC in test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, NMR-based biofluid screening can reveal characteristic metabolic events of ESCC and be feasible for early detection (ChiCTR2300073613). |
| Institute | Shantou University Medical College |
| Department | Radiology Department, Second Affiliated Hospital |
| Last Name | Lin |
| First Name | Yan |
| Address | No. 69, Dongxia North Road, Shantou, Guangdong, China |
| 994809889@qq.com | |
| Phone | +86 18823992148 |
| Submit Date | 2023-12-16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | GC/LC-MS |
| Release Date | 2024-02-08 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001876 |
| Project DOI: | doi: 10.21228/M87426 |
| Project Title: | NMR- and MS-based omics reveal characteristic metabolome atlas and optimize biofluid earlydiagnostic biomarkers for esophageal squamous cell carcinoma |
| Project Summary: | Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. We conducted NMR- and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- and one-week post-operative sera and urines from 560 participants across three hospitals, with machine learning, logistic regression and WGCNA. Aberrations in 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout the ESCC evolution, and were reflected in 16 serum and 10 urine metabolic signatures that were consistently identified by NMR and MS in both discovery and validation sets. NMR-based simplified panels of any five serum or urine metabolites outperformed clinical serological tumor markers (AUC = 0.984 and 0.930, respectively), and were effective in distinguishing early-stage ESCC in test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, NMR-based biofluid screening can reveal characteristic metabolic events of ESCC and be feasible for early detection (ChiCTR2300073613). |
| Institute: | Radiology Department, Second Affiliated Hospital, Shantou University Medical College |
| Last Name: | Lin |
| First Name: | Yan |
| Address: | No. 69, Dongxia North Road, Shantou, Guangdong, China |
| Email: | 994809889@qq.com |
| Phone: | +86 18823992148 |
Subject:
| Subject ID: | SU003141 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Fator |
|---|---|---|
| SA328039 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-13) | Early stage ESCC |
| SA328040 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-11) | Early stage ESCC |
| SA328041 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-14) | Early stage ESCC |
| SA328042 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-16) | Early stage ESCC |
| SA328043 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-1) | Early stage ESCC |
| SA328044 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-10) | Early stage ESCC |
| SA328045 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-15) | Early stage ESCC |
| SA328046 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-12) | Early stage ESCC |
| SA328047 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-4) | Early stage ESCC |
| SA328048 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-9) | Early stage ESCC |
| SA328049 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-2) | Early stage ESCC |
| SA328050 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-5) | Early stage ESCC |
| SA328051 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-3) | Early stage ESCC |
| SA328052 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-8) | Early stage ESCC |
| SA328053 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-7) | Early stage ESCC |
| SA328054 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-6) | Early stage ESCC |
| SA328055 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-28) | Normal tissue |
| SA328056 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-27) | Normal tissue |
| SA328057 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-29) | Normal tissue |
| SA328058 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-32) | Normal tissue |
| SA328059 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-26) | Normal tissue |
| SA328060 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-31) | Normal tissue |
| SA328061 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-30) | Normal tissue |
| SA328062 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-17) | Normal tissue |
| SA328063 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-20) | Normal tissue |
| SA328064 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-19) | Normal tissue |
| SA328065 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-18) | Normal tissue |
| SA328066 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-21) | Normal tissue |
| SA328067 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-22) | Normal tissue |
| SA328068 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-24) | Normal tissue |
| SA328069 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-23) | Normal tissue |
| SA328070 | measured concentration(Data07-BQ-ZY20221130-600MRM-RZZ-Sample-25) | Normal tissue |
| Showing results 1 to 32 of 32 |
Collection:
| Collection ID: | CO003134 |
| Collection Summary: | Tissue samples, including tumor and normal areas 5 cm away, were obtained under the guidance of experienced pathologists without compromising the patients' pathology examinations. The collected tissue was rinsed with PBS to avoid contamination, excess moisture was removed, and it was rapidly frozen in liquid nitrogen to arrest enzymatic or chemical reactions. Samples were stored at −80°C until metabolite extraction. |
| Collection Protocol Filename: | Tissue_collection_uploaded.pdf |
| Sample Type: | Tissue |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003150 |
| Treatment Summary: | None |
Sample Preparation:
| Sampleprep ID: | SP003147 |
| Sampleprep Summary: | For LC/MS-MS, 1000 μL of acetonitrile-methanol-H2O (2:2:1, containing isotope internal standards) was added to 50 mg samples. The samples were then homogenized, sonicated, and this process was repeated three times. After incubating the samples at -40 °C for 2 h, they were centrifuged at 12,000 rpm for 15 min at 4 °C. Subsequently, 800 μL of supernatant from each sample was transferred to a new EP tube and dried using a centrifugal concentrator. Next, 160 μL of 60% acetonitrile was added to reconstitute the dried samples. The mixture was vortexed for 30 s, and sonicated in an ice-water bath for 5 mins, followed by centrifugation at 12,000 rpm for 15 mins at 4 °C. Finally, 100 μL of supernatant from each sample was transferred into glass vials for LC-MS/MS analysis. |
Combined analysis:
| Analysis ID | AN004962 | AN004963 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Normal phase | Reversed phase |
| Chromatography system | Waters Acquity H-Class | Waters Acquity H-Class |
| Column | Waters ACQUITY UPLC BEH HILIC (150 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH HILIC (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 6500 QTrap | ABI Sciex 6500 QTrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | m/z | m/z |
Chromatography:
| Chromatography ID: | CH003745 |
| Instrument Name: | Waters Acquity H-Class |
| Column Name: | Waters ACQUITY UPLC BEH HILIC (150 x 2.1mm,1.7um) |
| Column Temperature: | 475°C |
| Flow Gradient: | 85% (vol/vol) B: 0.0 min, 85% B to 30% B:3.0 min, 30% B to 2% B:12.0 min, 2% B:15.0 min, 2% B to 85% B: 16.0 min, 85%: 23.0 min |
| Flow Rate: | Approximately 350–400 µl/min (back pressure should not exceed ~3,000 p.s.i. at 2% (vol/vol) B) |
| Solvent A: | ddH2O:Acetonitrile=8:2, 10 mmol/LAmmonium acetate |
| Solvent B: | Acetonitrile:ddH2O=9:1, 10 mmol/LAmmonium acetate |
| Chromatography Type: | Normal phase |
| Chromatography ID: | CH003746 |
| Instrument Name: | Waters Acquity H-Class |
| Column Name: | Waters ACQUITY UPLC BEH HILIC (150 x 2.1mm,1.7um) |
| Column Temperature: | 475°C |
| Flow Gradient: | 85% (vol/vol) B: 0.0 min, 85% B to 30% B:3.0 min, 30% B to 2% B:12.0 min, 2% B:15.0 min, 2% B to 85% B: 16.0 min, 85%: 23.0 min |
| Flow Rate: | Approximately 350–400 µl/min (back pressure should not exceed ~3,000 p.s.i. at 2% (vol/vol) B) |
| Solvent A: | ddH2O:Acetonitrile=8:2, 10 mmol/LAmmonium acetate |
| Solvent B: | Acetonitrile:ddH2O=9:1, 10 mmol/LAmmonium acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004702 |
| Analysis ID: | AN004962 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | All the MS data acquisition and quantitative analysis of target compounds in this project were completed by SCIEX Analyst Work Station Software (1.7.2) and BIOTREE Bio Bud (2.1.4). The final concentration CF (Final Concentration, μmol/L) was directly measured by the instrument. The concentration CC (Calculated Concentration, μmol/L) multiplied by the dilute release factor page 6 / 11 Dil (Dilution Factor), in μmol/L. The target metabolite concentration CM (Metabolite Concentration, nmol/g) in the sample is equal to the final measured concentration CF times the final sample volume VF (Volume, μL) and the concentration factor CF of the sample during the pretreatment process, divided by the sample mass MS (Weight, mg), in nmol/g. NA indicated that no target metabolites were detected in the sample. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004703 |
| Analysis ID: | AN004963 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | All the MS data acquisition and quantitative analysis of target compounds in this project were completed by SCIEX Analyst Work Station Software (1.7.2) and BIOTREE Bio Bud (2.1.4). The final concentration CF (Final Concentration, μmol/L) was directly measured by the instrument. The concentration CC (Calculated Concentration, μmol/L) multiplied by the dilute release factor page 6 / 11 Dil (Dilution Factor), in μmol/L. The target metabolite concentration CM (Metabolite Concentration, nmol/g) in the sample is equal to the final measured concentration CF times the final sample volume VF (Volume, μL) and the concentration factor CF of the sample during the pretreatment process, divided by the sample mass MS (Weight, mg), in nmol/g. NA indicated that no target metabolites were detected in the sample. |
| Ion Mode: | NEGATIVE |
