#METABOLOMICS WORKBENCH pengfeixu_njmu_20241022_191054 DATATRACK_ID:5304 STUDY_ID:ST003579 ANALYSIS_ID:AN005877 PROJECT_ID:PR002209 VERSION 1 CREATED_ON November 15, 2024, 4:28 am #PROJECT PR:PROJECT_TITLE Landscape of Metabolic Fingerprinting for Diagnosis of Ovarian Endometriosis. PR:PROJECT_SUMMARY The prevalence of Ovarian Endometriosis (OvE) is notably high, especially among PR:PROJECT_SUMMARY young females. However, the current diagnostic approaches for OvE remain PR:PROJECT_SUMMARY inadequate. In this study, We employed untargeted ultra-high performance liquid PR:PROJECT_SUMMARY chromatography-MS/MS (UHPLC-MS/MS) to examine the metabolomic profiles in the PR:PROJECT_SUMMARY serum samples of 34 OvE patients and 34 healthy control (HC) female PR:PROJECT_SUMMARY participants. Based on the untargeted UHPLC-MS/MS results, we identified 612 PR:PROJECT_SUMMARY metabolites were included in the current analysis, Among them, 56 endogenous PR:PROJECT_SUMMARY metabolites that were differently expressed between the OvE patients and HC PR:PROJECT_SUMMARY women. These metabolites can provide a preliminary basis for a panel of serum PR:PROJECT_SUMMARY metabolites potentially implicated in OvE. PR:INSTITUTE Women’s Hospital of Nanjing Medical University PR:LAST_NAME Xu PR:FIRST_NAME Pengfei PR:ADDRESS No.123, Tianfei Lane, Mochou Road, Qinhuai District PR:EMAIL pengfeixu@njmu.edu.cn PR:PHONE 15950538206 #STUDY ST:STUDY_TITLE Landscape of Metabolic Fingerprinting for Diagnosis of Ovarian Endometriosis. ST:STUDY_SUMMARY The prevalence of Ovarian Endometriosis (OvE) is notably high, especially among ST:STUDY_SUMMARY young females. However, the current diagnostic approaches for OvE remain ST:STUDY_SUMMARY inadequate. In this study, We employed untargeted ultra-high performance liquid ST:STUDY_SUMMARY chromatography-MS/MS (UHPLC-MS/MS) to examine the metabolomic profiles in the ST:STUDY_SUMMARY serum samples of 34 OvE patients and 34 healthy control (HC) female ST:STUDY_SUMMARY participants. Based on the untargeted UHPLC-MS/MS results, we identified 612 ST:STUDY_SUMMARY metabolites were included in the current analysis, Among them, 56 endogenous ST:STUDY_SUMMARY metabolites that were differently expressed between the OvE patients and HC ST:STUDY_SUMMARY women. These metabolites can provide a preliminary basis for a panel of serum ST:STUDY_SUMMARY metabolites potentially implicated in OvE. ST:INSTITUTE Women’s Hospital of Nanjing Medical University ST:LAST_NAME Xu ST:FIRST_NAME Pengfei ST:ADDRESS No.123, Tianfei Lane, Mochou Road, Qinhuai District ST:EMAIL pengfeixu@njmu.edu.cn ST:PHONE 15950538206 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:GENDER Female #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - CON-1 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-1.mzML SUBJECT_SAMPLE_FACTORS - CON-2 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-2.mzML SUBJECT_SAMPLE_FACTORS - CON-3 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-3.mzML SUBJECT_SAMPLE_FACTORS - CON-4 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-4.mzML SUBJECT_SAMPLE_FACTORS - CON-5 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-5.mzML SUBJECT_SAMPLE_FACTORS - CON-6 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-6.mzML SUBJECT_SAMPLE_FACTORS - CON-7 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-7.mzML SUBJECT_SAMPLE_FACTORS - CON-8 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-8.mzML SUBJECT_SAMPLE_FACTORS - CON-9 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-9.mzML SUBJECT_SAMPLE_FACTORS - CON-10 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-10.mzML SUBJECT_SAMPLE_FACTORS - CON-11 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-11.mzML SUBJECT_SAMPLE_FACTORS - CON-12 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-12.mzML SUBJECT_SAMPLE_FACTORS - CON-13 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-13.mzML SUBJECT_SAMPLE_FACTORS - CON-14 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-14.mzML SUBJECT_SAMPLE_FACTORS - CON-15 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-15.mzML SUBJECT_SAMPLE_FACTORS - CON-16 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-16.mzML SUBJECT_SAMPLE_FACTORS - CON-17 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-17.mzML SUBJECT_SAMPLE_FACTORS - CON-18 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-18.mzML SUBJECT_SAMPLE_FACTORS - CON-19 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-19.mzML SUBJECT_SAMPLE_FACTORS - CON-20 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-20.mzML SUBJECT_SAMPLE_FACTORS - CON-21 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-21.mzML SUBJECT_SAMPLE_FACTORS - CON-22 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-22.mzML SUBJECT_SAMPLE_FACTORS - CON-23 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-23.mzML SUBJECT_SAMPLE_FACTORS - CON-24 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-24.mzML SUBJECT_SAMPLE_FACTORS - CON-25 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-25.mzML SUBJECT_SAMPLE_FACTORS - CON-26 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-26.mzML SUBJECT_SAMPLE_FACTORS - CON-27 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-27.mzML SUBJECT_SAMPLE_FACTORS - CON-28 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-28.mzML SUBJECT_SAMPLE_FACTORS - CON-29 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-29.mzML SUBJECT_SAMPLE_FACTORS - CON-30 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-30.mzML SUBJECT_SAMPLE_FACTORS - CON-31 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-31.mzML SUBJECT_SAMPLE_FACTORS - CON-32 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-32.mzML SUBJECT_SAMPLE_FACTORS - CON-33 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-33.mzML SUBJECT_SAMPLE_FACTORS - CON-34 Group:Control | Sample source:serum RAW_FILE_NAME(Raw file name)=CON-34.mzML SUBJECT_SAMPLE_FACTORS - LI Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=LI.mzML SUBJECT_SAMPLE_FACTORS - 21215546 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21215546.mzML SUBJECT_SAMPLE_FACTORS - 21215782 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21215782.mzML SUBJECT_SAMPLE_FACTORS - 21216212 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21216212.mzML SUBJECT_SAMPLE_FACTORS - 21216372 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21216372.mzML SUBJECT_SAMPLE_FACTORS - 21216513 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21216513.mzML SUBJECT_SAMPLE_FACTORS - 21216514 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21216514.mzML SUBJECT_SAMPLE_FACTORS - 21216532 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21216532.mzML SUBJECT_SAMPLE_FACTORS - 21217191 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21217191.mzML SUBJECT_SAMPLE_FACTORS - 21217800-PANXIAOXIA Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21217800-PANXIAOXIA.mzML SUBJECT_SAMPLE_FACTORS - 21217803-LIQING Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21217803-LIQING.mzML SUBJECT_SAMPLE_FACTORS - 21217910 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21217910.mzML SUBJECT_SAMPLE_FACTORS - 21218133-CHENJIE Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21218133-CHENJIE.mzML SUBJECT_SAMPLE_FACTORS - 21218201 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21218201.mzML SUBJECT_SAMPLE_FACTORS - 21218999 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21218999.mzML SUBJECT_SAMPLE_FACTORS - 21219036 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21219036.mzML SUBJECT_SAMPLE_FACTORS - 21219095 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21219095.mzML SUBJECT_SAMPLE_FACTORS - 21219147 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=21219147.mzML SUBJECT_SAMPLE_FACTORS - 22200036 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22200036.mzML SUBJECT_SAMPLE_FACTORS - 22200039 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22200039.mzML SUBJECT_SAMPLE_FACTORS - 22200425 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22200425.mzML SUBJECT_SAMPLE_FACTORS - 22200612 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22200612.mzML SUBJECT_SAMPLE_FACTORS - 22201099 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22201099.mzML SUBJECT_SAMPLE_FACTORS - 22201109 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22201109.mzML SUBJECT_SAMPLE_FACTORS - 22201601-CHENYANTING Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22201601-CHENYANTING.mzML SUBJECT_SAMPLE_FACTORS - 22201611-LIU Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22201611-LIU.mzML SUBJECT_SAMPLE_FACTORS - 22202005 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22202005.mzML SUBJECT_SAMPLE_FACTORS - 22202784 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22202784.mzML SUBJECT_SAMPLE_FACTORS - 22202910 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22202910.mzML SUBJECT_SAMPLE_FACTORS - 22202946-WANGQUAN Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22202946-WANGQUAN.mzML SUBJECT_SAMPLE_FACTORS - 22203272 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22203272.mzML SUBJECT_SAMPLE_FACTORS - 22203743 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22203743.mzML SUBJECT_SAMPLE_FACTORS - 22203919 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22203919.mzML SUBJECT_SAMPLE_FACTORS - 22204071 Group:Ovarian endometriosis | Sample source:serum RAW_FILE_NAME(Raw file name)=22204071.mzML #COLLECTION CO:COLLECTION_SUMMARY All participants were obtain from Women’s Hospital of Nanjing Medical CO:COLLECTION_SUMMARY university. Patients diagnosed with Ovarian Endometriosis (OvE) in the CO:COLLECTION_SUMMARY Department of Gynecology of Women’s Hospital of Nanjing Medical university CO:COLLECTION_SUMMARY from December 1, 2021, to December 1, 2023were recruited.. All these OvE CO:COLLECTION_SUMMARY patients accepted the laparoscopy, and the diagnosis of OvE was confirmed by CO:COLLECTION_SUMMARY pathologists. During the same period, we also recruited healthy female CO:COLLECTION_SUMMARY volunteers who receive physical examination in our hospital. These people had no CO:COLLECTION_SUMMARY chronic illnesses, no history of medications and no abnormalities in pelvic CO:COLLECTION_SUMMARY examinations. (1) People who are diagnosed with Pregnant or lactating women; (2) CO:COLLECTION_SUMMARY Aged younger than 18 years or over 50 years; (3) History of drug treatment CO:COLLECTION_SUMMARY within 3 months; (4) Patients complicated by other diseases (e.g., CO:COLLECTION_SUMMARY hyperthyroidism, hypothyroidism, diabetes mellitus, hypertension); (6) Disagree CO:COLLECTION_SUMMARY to participate in the study or uncooperative to the researchists; (7) Clinical CO:COLLECTION_SUMMARY data were not available from the cohort.All human subjects gave written informed CO:COLLECTION_SUMMARY consent, and all human studies performed abided by the Declaration of Helsinki. CO:COLLECTION_SUMMARY the ethics committee of Women’s Hospital of Nanjing Medical University CO:COLLECTION_SUMMARY approved all study protocols (No.2022KY-100). Blood samples of OvE patients were CO:COLLECTION_SUMMARY collected before the operation. All participants donated their blood samples CO:COLLECTION_SUMMARY after fasting overnight for more than 8 hours. The samples were centrifuged CO:COLLECTION_SUMMARY immediately，and the upper serum were separated and stored at -80°C. CO:SAMPLE_TYPE Blood (serum) #TREATMENT TR:TREATMENT_SUMMARY / #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Untargeted metabolomics measurements in serum were performed using MetabolonTM SP:SAMPLEPREP_SUMMARY Discovery HD4 platform. Briefly, this platform consisted of 4 independent SP:SAMPLEPREP_SUMMARY ultra-high-performance liquid chromatography-tandem mass spectrometry SP:SAMPLEPREP_SUMMARY (UPLC-MS/MS) methods: two separate reversed phases (RP)/UPLC-MS/MS methods with SP:SAMPLEPREP_SUMMARY positive ion mode electrospray ionization (ESI), RP/UPLC-MS/MS with negative ion SP:SAMPLEPREP_SUMMARY mode ESI, and hydrophilic interaction liquid chromatography (HILIC)/UPLC-MS/MS SP:SAMPLEPREP_SUMMARY with negative ion mode ESI. Metabolites with missingness less than 10% were SP:SAMPLEPREP_SUMMARY included, and missing values were imputed using half of the minimum within each SP:SAMPLEPREP_SUMMARY metabolite. Finally, 612 metabolites were included in the current analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Ultra-performance liquid chromatography separation CH:INSTRUMENT_NAME Agilent 1290 Infinity CH:COLUMN_NAME Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) CH:SOLVENT_A 100% Water; 0.1 % Formic acid CH:SOLVENT_B 100% Acetonitrile; 0.1% Formic acid CH:FLOW_GRADIENT 0-1 min，90- 70% B; 1-19 min，70- 5% B; 19-20 min，5% B;20-25 min，95% B CH:FLOW_RATE 0.4 mL/min CH:COLUMN_TEMPERATURE 40℃ #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Ultra-performance liquid chromatography separation was performed using a 1290 MS:MS_COMMENTS Infinity LC System equipped with a C18 chromatographic column (2.6 µm, 100 × MS:MS_COMMENTS 2.1 mm). The mobile phase consisted of 0.1 % formic acid in water (A) and 0.1 % MS:MS_COMMENTS formic acid in acetonitrile (B). The analysis was conducted using an elution MS:MS_COMMENTS gradient procedure as follows: 0–1 min, 90–70 % B; 1–19 min, 70–5 % B; MS:MS_COMMENTS 19–20 min, 5 % B; and 20–25 min, 95 % B. The column temperature was set at MS:MS_COMMENTS 40 ◦C, the autosampler temperature was set at 4 ◦C, the flow rate was set at MS:MS_COMMENTS 0.4 ml/min, and the injection volume was set at 5 µL. Q-Exactive Orbitrap MS:MS_COMMENTS tandem mass spectrometry (Thermo Fisher Scientific Technologies) was used to MS:MS_COMMENTS determine the plasma global metabolite profile in the information-dependent MS:MS_COMMENTS acquisition mode with simultaneous acquisition in positive ion mode and negative MS:MS_COMMENTS ion mode and secondary fragmentation of the top 10 precursor ions in one cycle MS:MS_COMMENTS to acquire MS/MS spectra. The scan range was 30–1000 Da. Quality control (QC) MS:MS_COMMENTS samples were prepared by mixing equal-volume aliquots of the samples and MS:MS_COMMENTS interspersing them in the sample sequence to monitor the stability of the MS:MS_COMMENTS instrument and evaluate the reliability of the experimental data. The MS:MS_COMMENTS electrospray ion (ESI) source conditions were set as follows: ion source gas, 1; MS:MS_COMMENTS ion source gas, 40 psi; ion source gas, 2; curtain gas, 30 psi; and drying MS:MS_COMMENTS temperature, 550 ◦C. The collision energy, delustering potential, and ion MS:MS_COMMENTS spray voltage were set to 30 V, 80 V, and 5200 V, respectively, for positive MS:MS_COMMENTS mode and −30 V, −50 V, and −5200 V, respectively, for negative mode. MS:MS_COMMENTS Metabolites with missingness less than 10% were included, and missing values MS:MS_COMMENTS were imputed using half of the minimum within each metabolite. Finally, 612 MS:MS_COMMENTS metabolites were included in the current analysis. MS:MS_RESULTS_FILE ST003579_AN005877_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END