Summary of Study ST001937
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 PR001226. The data can be accessed directly via it's Project DOI: 10.21228/M87H88 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 | ST001937 |
| Study Title | Comprehensive plasma metabolomics and lipidomics based management of benign and malignant solitary pulmonary nodules |
| Study Summary | This study found evidence of early metabolic alterations that can distinguish SPNs from healthy controls, but not for benign and malignant SPNs (lung cancer in stage I), highlighting that malignant SPNs less than 3 cm in diameter are most likely lung cancer at some early stage that does not affect blood circulation. Benign SPNs seldom require excessive treatment, and the strategy to detecting and managing malignant SPNs is to perform periodic radiographic examinations and, if operable, bring patients to surgery as quickly as feasible to prevent cancer cells from entering the circulation. |
| Institute | China Pharmaceutical University |
| Last Name | Zhou |
| First Name | Wei |
| Address | NO.639 Longmian avenue, Jiangning District, Nanjing city, Jiangsu Province, China |
| wzhou@cpu.edu.cn | |
| Phone | 18351893063 |
| Submit Date | 2021-09-11 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2023-09-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001226 |
| Project DOI: | doi: 10.21228/M87H88 |
| Project Title: | Comprehensive plasma metabolomics and lipidomics based management of benign and malignant solitary pulmonary nodules |
| Project Summary: | A discovery set and four validation sets were used in our study to confirm and validate the results for differentiating benign from malignant SPNs. |
| Institute: | China Pharmaceutical University |
| Last Name: | Zhou |
| First Name: | Wei |
| Address: | NO.639 Longmian Avenue, Jiangning District, Nanjing city, Jiangsu Province, China |
| Email: | wzhou@cpu.edu.cn |
| Phone: | 18351893063 |
Subject:
| Subject ID: | SU002015 |
| 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 | Pheotypes |
|---|---|---|
| SA181969 | WH10 | Benign SPNS |
| SA181970 | WH18 | Benign SPNS |
| SA181971 | WH9 | Benign SPNS |
| SA181972 | WH31 | Benign SPNS |
| SA181973 | WH5 | Benign SPNS |
| SA181974 | WH3 | Benign SPNS |
| SA181975 | WH4 | Benign SPNS |
| SA181976 | WH34 | Benign SPNS |
| SA181977 | WH7 | Benign SPNS |
| SA181978 | WH39 | Benign SPNS |
| SA181979 | SZ20 | Benign SPNS |
| SA181980 | SZ23 | Benign SPNS |
| SA181981 | SZ34 | Benign SPNS |
| SA181982 | SZ18 | Benign SPNS |
| SA181983 | SZ3 | Benign SPNS |
| SA181984 | WH1 | Benign SPNS |
| SA181985 | WH45 | Benign SPNS |
| SA181986 | SZ1 | Benign SPNS |
| SA181987 | WH38 | Benign SPNS |
| SA181988 | JY1679 | Benign SPNS |
| SA181989 | JY1252 | Benign SPNS |
| SA181990 | JY1347 | Benign SPNS |
| SA181991 | JY1356 | Benign SPNS |
| SA181992 | JY1188 | Benign SPNS |
| SA181993 | JY1149 | Benign SPNS |
| SA181994 | JY1104 | Benign SPNS |
| SA181995 | JY1135 | Benign SPNS |
| SA181996 | JY1144 | Benign SPNS |
| SA181997 | JY1363 | Benign SPNS |
| SA181998 | JY1377 | Benign SPNS |
| SA181999 | JY1660 | Benign SPNS |
| SA182000 | JY1676 | Benign SPNS |
| SA182001 | SZ35 | Benign SPNS |
| SA182002 | JY1637 | Benign SPNS |
| SA182003 | JY1616 | Benign SPNS |
| SA182004 | JY1393 | Benign SPNS |
| SA182005 | JY1479 | Benign SPNS |
| SA182006 | JY1601 | Benign SPNS |
| SA182007 | JY1715 | Benign SPNS |
| SA182008 | SZ39 | Benign SPNS |
| SA182009 | SZ156 | Benign SPNS |
| SA182010 | SZ159 | Benign SPNS |
| SA182011 | SZ167 | Benign SPNS |
| SA182012 | SZ153 | Benign SPNS |
| SA182013 | SZ135 | Benign SPNS |
| SA182014 | SZ122 | Benign SPNS |
| SA182015 | SZ125 | Benign SPNS |
| SA182016 | SZ130 | Benign SPNS |
| SA182017 | SZ176 | Benign SPNS |
| SA182018 | SZ214 | Benign SPNS |
| SA182019 | 2SZ4 | Benign SPNS |
| SA182020 | 2SZ27 | Benign SPNS |
| SA182021 | 2JY8 | Benign SPNS |
| SA182022 | SZ244 | Benign SPNS |
| SA182023 | SZ233 | Benign SPNS |
| SA182024 | SZ219 | Benign SPNS |
| SA182025 | SZ227 | Benign SPNS |
| SA182026 | SZ232 | Benign SPNS |
| SA182027 | SZ120 | Benign SPNS |
| SA182028 | SZ119 | Benign SPNS |
| SA182029 | SZ60 | Benign SPNS |
| SA182030 | SZ62 | Benign SPNS |
| SA182031 | SZ69 | Benign SPNS |
| SA182032 | SZ55 | Benign SPNS |
| SA182033 | SZ45 | Benign SPNS |
| SA182034 | SZ43 | Benign SPNS |
| SA182035 | SZ44 | Benign SPNS |
| SA182036 | SZ48 | Benign SPNS |
| SA182037 | SZ75 | Benign SPNS |
| SA182038 | SZ79 | Benign SPNS |
| SA182039 | SZ100 | Benign SPNS |
| SA182040 | SZ105 | Benign SPNS |
| SA182041 | SZ114 | Benign SPNS |
| SA182042 | SZ91 | Benign SPNS |
| SA182043 | SZ87 | Benign SPNS |
| SA182044 | SZ82 | Benign SPNS |
| SA182045 | SZ85 | Benign SPNS |
| SA182046 | JY1020 | Benign SPNS |
| SA182047 | SZ194 | Benign SPNS |
| SA182048 | XH125 | Benign SPNS |
| SA182049 | XH168 | Benign SPNS |
| SA182050 | XH197 | Benign SPNS |
| SA182051 | XH122 | Benign SPNS |
| SA182052 | XH119 | Benign SPNS |
| SA182053 | XH66 | Benign SPNS |
| SA182054 | XH96 | Benign SPNS |
| SA182055 | XH99 | Benign SPNS |
| SA182056 | XH203 | Benign SPNS |
| SA182057 | XH216 | Benign SPNS |
| SA182058 | XH282 | Benign SPNS |
| SA182059 | 2XH45 | Benign SPNS |
| SA182060 | 2XH48 | Benign SPNS |
| SA182061 | XH272 | Benign SPNS |
| SA182062 | XH261 | Benign SPNS |
| SA182063 | XH241 | Benign SPNS |
| SA182064 | XH243 | Benign SPNS |
| SA182065 | XH245 | Benign SPNS |
| SA182066 | XH62 | Benign SPNS |
| SA182067 | XH56 | Benign SPNS |
| SA182068 | 2JY21 | Benign SPNS |
Collection:
| Collection ID: | CO002008 |
| Collection Summary: | A total of 1160 plasma samples was obtained from healthy volunteers (n=280), benign SPNs (n=157, center 1=42; center 2=23; center 3=45; center 4=13; center 5=34) and malignant SPNs (stage I, n=723, center 1=118; center 2=105; center 3=139; center 4=33; center 5=328) patients enrolled from 5 independent centers. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR002027 |
| Treatment Summary: | Without treatment |
Sample Preparation:
| Sampleprep ID: | SP002021 |
| Sampleprep Summary: | To undertake comprehensive lipidomic profiling, a sample preparation approach for serum based on liquid-liquid MTBE extraction was utilized to cover diverse classes of lipids. Untargeted lipidomic analysis was performed using a Dionex UltiMate 3000 UHPLC system (Santa Clara, CA, USA) linked online via electrospray ionization source (ESI) with a Q ExactiveTM Hybrid Quadrupole-OrbitrapTM Mass Spectrometer (Thermo Fisher Scientific, Inc., MA, USA). Comprehensive metabolomic analysis was performed on a TRACE 1310 gas chromatograph equipped with an AS 1310 autosampler connected to a TSQ 8000 triple quadrupole mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) as described previously 14. |
| Sampleprep Protocol ID: | 346 Lipidomics_LCMSProtocol.pdf |
Combined analysis:
| Analysis ID | AN003150 |
|---|---|
| Analysis type | MS |
| Chromatography type | Unspecified |
| Chromatography system | Thermo Trace 1310/Dionex UltiMate 3000 UHPLC |
| Column | TG-5MS |
| MS Type | EI/ESI |
| MS instrument type | Triple quadrupole/Orbitrap |
| MS instrument name | Thermo TSQ 8000/Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | peak height |
Chromatography:
| Chromatography ID: | CH002330 |
| Instrument Name: | Thermo Trace 1310/Dionex UltiMate 3000 UHPLC |
| Column Name: | TG-5MS |
| Chromatography Type: | Unspecified |
MS:
| MS ID: | MS002930 |
| Analysis ID: | AN003150 |
| Instrument Name: | Thermo TSQ 8000/Thermo Q Exactive Orbitrap |
| Instrument Type: | Triple quadrupole/Orbitrap |
| MS Type: | EI/ESI |
| MS Comments: | The raw data files from LC-MS were converted into Analysis Base File (ABF) format by Abf Converter (http://www.reifycs.com/AbfConverter). Then, using the open-source program MS-Dial v.4.24 15, the automatic peak selecting, integration, retention time adjustment by the aforementioned database, and alignment were performed. The retention time index (RI) tolerance in GC-MS was 3,000, while the peak height threshold was 10,000. In LC-MS, the peak height threshold was 1,000,000 in positive ion mode and 500,000 in negative ion mode. The resultant output data table of high quality time-aligned investigated metabolites, together with their related RT, m/z, and peak height acquired for each sample, was statistically analyzed. All metabolite identifications were manually double-checked. |
| Ion Mode: | POSITIVE |
