Summary of Study ST001937

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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.

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Study IDST001937
Study TitleComprehensive plasma metabolomics and lipidomics based management of benign and malignant solitary pulmonary nodules
Study SummaryThis 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.
China Pharmaceutical University
Last NameZhou
First NameWei
AddressNO.639 Longmian avenue, Jiangning District, Nanjing city, Jiangsu Province, China
Submit Date2021-09-11
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailGC-MS/LC-MS
Release Date2023-09-11
Release Version1
Wei Zhou Wei Zhou application/zip

Select appropriate tab below to view additional metadata details:


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


Subject ID:SU002015
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606


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

mb_sample_id local_sample_id Pheotypes
SA181969WH10Benign SPNS
SA181970WH18Benign SPNS
SA181971WH9Benign SPNS
SA181972WH31Benign SPNS
SA181973WH5Benign SPNS
SA181974WH3Benign SPNS
SA181975WH4Benign SPNS
SA181976WH34Benign SPNS
SA181977WH7Benign SPNS
SA181978WH39Benign SPNS
SA181979SZ20Benign SPNS
SA181980SZ23Benign SPNS
SA181981SZ34Benign SPNS
SA181982SZ18Benign SPNS
SA181983SZ3Benign SPNS
SA181984WH1Benign SPNS
SA181985WH45Benign SPNS
SA181986SZ1Benign SPNS
SA181987WH38Benign SPNS
SA181988JY1679Benign SPNS
SA181989JY1252Benign SPNS
SA181990JY1347Benign SPNS
SA181991JY1356Benign SPNS
SA181992JY1188Benign SPNS
SA181993JY1149Benign SPNS
SA181994JY1104Benign SPNS
SA181995JY1135Benign SPNS
SA181996JY1144Benign SPNS
SA181997JY1363Benign SPNS
SA181998JY1377Benign SPNS
SA181999JY1660Benign SPNS
SA182000JY1676Benign SPNS
SA182001SZ35Benign SPNS
SA182002JY1637Benign SPNS
SA182003JY1616Benign SPNS
SA182004JY1393Benign SPNS
SA182005JY1479Benign SPNS
SA182006JY1601Benign SPNS
SA182007JY1715Benign SPNS
SA182008SZ39Benign SPNS
SA182009SZ156Benign SPNS
SA182010SZ159Benign SPNS
SA182011SZ167Benign SPNS
SA182012SZ153Benign SPNS
SA182013SZ135Benign SPNS
SA182014SZ122Benign SPNS
SA182015SZ125Benign SPNS
SA182016SZ130Benign SPNS
SA182017SZ176Benign SPNS
SA182018SZ214Benign SPNS
SA1820192SZ4Benign SPNS
SA1820202SZ27Benign SPNS
SA1820212JY8Benign SPNS
SA182022SZ244Benign SPNS
SA182023SZ233Benign SPNS
SA182024SZ219Benign SPNS
SA182025SZ227Benign SPNS
SA182026SZ232Benign SPNS
SA182027SZ120Benign SPNS
SA182028SZ119Benign SPNS
SA182029SZ60Benign SPNS
SA182030SZ62Benign SPNS
SA182031SZ69Benign SPNS
SA182032SZ55Benign SPNS
SA182033SZ45Benign SPNS
SA182034SZ43Benign SPNS
SA182035SZ44Benign SPNS
SA182036SZ48Benign SPNS
SA182037SZ75Benign SPNS
SA182038SZ79Benign SPNS
SA182039SZ100Benign SPNS
SA182040SZ105Benign SPNS
SA182041SZ114Benign SPNS
SA182042SZ91Benign SPNS
SA182043SZ87Benign SPNS
SA182044SZ82Benign SPNS
SA182045SZ85Benign SPNS
SA182046JY1020Benign SPNS
SA182047SZ194Benign SPNS
SA182048XH125Benign SPNS
SA182049XH168Benign SPNS
SA182050XH197Benign SPNS
SA182051XH122Benign SPNS
SA182052XH119Benign SPNS
SA182053XH66Benign SPNS
SA182054XH96Benign SPNS
SA182055XH99Benign SPNS
SA182056XH203Benign SPNS
SA182057XH216Benign SPNS
SA182058XH282Benign SPNS
SA1820592XH45Benign SPNS
SA1820602XH48Benign SPNS
SA182061XH272Benign SPNS
SA182062XH261Benign SPNS
SA182063XH241Benign SPNS
SA182064XH243Benign SPNS
SA182065XH245Benign SPNS
SA182066XH62Benign SPNS
SA182067XH56Benign SPNS
SA1820682JY21Benign SPNS
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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 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 instrument type Triple quadrupole/Orbitrap
MS instrument name Thermo TSQ 8000/Thermo Q Exactive Orbitrap
Units peak height


Chromatography ID:CH002330
Instrument Name:Thermo Trace 1310/Dionex UltiMate 3000 UHPLC
Column Name:TG-5MS
Chromatography Type:Unspecified


MS ID:MS002930
Analysis ID:AN003150
Instrument Name:Thermo TSQ 8000/Thermo Q Exactive Orbitrap
Instrument Type:Triple quadrupole/Orbitrap
MS Comments:The raw data files from LC-MS were converted into Analysis Base File (ABF) format by Abf Converter ( 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.