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Clinical Cohorts/Identification/GBC/GBC_20_MSMS_30PE27PC.raw/_FUNC014.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/LC/LC_20_PB MSMS_30PE27PC.raw/_FUNC017.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/GBC/GBC_21_PB MSMS_10PE15PC.raw/_FUNC004.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BC_L/BC_L_21_MSMS_10PE10PC.raw/_FUNC018.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BBC/BBC_19_MSMS_10PE10PC.raw/_FUNC001.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BC_L/BC_L_20_PB MSMS_30PE27PC.raw/_FUNC004.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BBC/BBC_20_MSMS_10PE10PC.raw/_CHRO001.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BBC/BBC_19_PB MSMS_20PE20PC.raw/_FUNC009.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BC_L/BC_L_20_PB MSMS_20PE20PC.raw/_FUNC020.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BC_L/BC_L_21_MSMS_10PE10PC.raw/_FUNC009.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/LC/LC_20_PB MSMS_10PE10PC.raw/_CHRO003.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BBC/BBC_19_MSMS_10PE10PC.raw/_FUNC010.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BBC/BBC_20_MSMS_30PE27PC.raw/_FUNC015.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/GBC/GBC_21_PB MSMS_10PE15PC.raw/_FUNC013.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BBC/BBC_19_MSMS_20PE20PC.raw/_CHRO002.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BC_L/BC_L_21_PB MSMS_10PE10PC.raw/_FUNC003.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/LC/LC_19_PB MSMS_20PE20PC.raw/_FUNC002.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/GBC/GBC_20_MSMS_30PE27PC.raw/_FUNC005.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/BBC/BBC_21_PB MSMS_30PE27PC.raw/_FUNC003.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/LC/LC_19_MSMS_10PE10PC.raw/_FUNC019.DATftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170/FILES/PB reaction 105 Clinical Cohorts/Identification/GBC/GBC_20_MSMS_15PE15PC.raw/_FUNC002.DATprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10170<p>Annotation of lipid content was performed with LipidIN. Data from the Orbitrap Exploris 240 utilized MS1 tolerance of 10 ppm and MS2 tolerance of 20 ppm, while data from the Agilent 6546 Q-TOF was set to MS1 tolerance of 20 ppm and MS2 tolerance of 40 ppm. By taking the relatively low precision associated with the Paternò-Büchi reaction into account, data from the Xevo G2-XS Q-TOF was configured with MS1 tolerance of 1000 ppm and MS2 tolerance of 40 ppm.</p>MetaboLightsPublicLiquid Chromatography MS - negative - reverse phaseLiquid Chromatography MS - alternating - reverse phaseLiquid Chromatography MS - positive - reverse phase<p>7600 EAD samples</p><p>The liquid chromatography conditions specify the use of the Exion LC system and the chromatography column used is a Kinetex C18 100 Å (2.6 µm, 2.1 mm x 100 mm; Phenomenex). The composition of mobile phase A: methanol, acetonitrile, and water mixed in a 1:1:1 ratio, containing 5 mM ammonium acetate. The composition of mobile phase B is: isopropanol containing 5 mM ammonium acetate. Gradient elution time, lasting 17 min. The flow rate is 0.3 mL/min. The injection volume is 2 µL.</p><p>&nbsp;</p><p>P-B reaction samples</p><p>The samples were separated using an ACQUITY UPLC I-Class PLUS ultra-high-performance liquid chromatography system and an ACQUITY UPLC BEH HILIC (1.7 µm, 2.1 mm x 100 mm; Waters). The column temperature was maintained at 30 °C, and the flow rate was set at 0.35 mL/min. The mobile phase composition was as follows: A, a 10 mmol ammonium acetate aqueous solution (containing 0.2% acetic acid), and B, a mixture of acetonitrile/acetone/isopropanol (50/48/2, v/v/v). The gradient elution program was as follows: 0 to 2.4 min, 90% to 85% B; 2.4 to 3.2 min, 85% to 80% B; 3.2 to 5 min, 80% B; 5.0 to 5.1 min, 80% to 70% B; 5.1 to 6 min, 70% B; 6 to 6.1 min, 70% to 90% B; 6.1 to 10.0 min, 90% B. Throughout the analysis, samples were kept in an automatic sampler at 6 °C.</p><p>&nbsp;</p><p>105 case MS/MS samples (Cohort3)</p><p>The instrument was an Agilent 1290 LC, with a Waters Acquity CSH C18 column, 1.7 µm. The mobile phase A was a mixture of methanol/acetonitrile/water in a ratio of 50:40:10 containing 10 mM ammonium formate. The mobile phase B was a mixture of 2-propanol/water in a ratio of 95:5 containing 10 mM ammonium formate. The elution gradient was a 26-min gradient elution. The flow rate was 210-250 µL/min. The injection volume was 4 µL for positive ions and 12 µL for negative ions. The column temperature was 40 °C.</p><p>&nbsp;</p><p>335 case MS/MS samples (Cohort2)</p><p>A Waters ACQUITY UPLC system and an ACQUITY UPLC BEH C8 (1.7 µm, 2.1 mm x 100 mm; Waters) column were used. Mobile phase A was composed of 40% water and 60% acetonitrile. Mobile phase B was composed of 90% isopropanol and 10% acetonitrile. 2 mM ammonium formate was added to both mobile phases to improve ionization.&nbsp;LC began with 15.5 min of 32% B at 0.26 mL/min, the mobile phase gradient began with 32% B to 85% B over 14 min, then from 85% B to 97% B only 0.1 min. Maintained at 97% B for 2.4 min, then switched to 32% B for 0.1 min and maintained 4.9 min. Each reconstitution solvent contains a series of standards at fixed concentrations to ensure injection and chromatographic consistency. The standards consist of TG 45;0 (1 µg/mL), FFA-d3 18:0 (1 µg/mL), FFA-d3 16:0 (1 µg/mL), SM 12;0 (1 µg/mL), PE 30;0 (1 µg/mL), PC 19:0 (1 µg/mL), D27-FA (1 µg/mL), Cer 17;0 (1µg/mL).</p><p><br></p><p>1500 case MS/MS samples (Cohort1)</p><p>A Waters ACQUITY UPLC system and an ACQUITY UPLC BEH C8 (1.7 µm, 2.1 mm x 100 mm; Waters) column were used. Mobile phase A was composed of 40% water and 60% acetonitrile. Mobile phase B was composed of 90% isopropanol and 10% acetonitrile. 10 mM ammonium formate was added to both mobile phases to improve ionization.&nbsp;LC began with 1.5 min of 32% B at 0.26 mL/min, the mobile phase gradient began with 32% B to 85% B over 15.5 min, then from 85% B to 97% B only 0.1 min. Maintained at 97% B for 2.4 min, then switched to 32% B for 0.1 min and maintained 1.9 min. Each reconstitution solvent contains a series of standards at fixed concentrations to ensure injection and chromatographic consistency. The standards consist of TG 45;0 (0.67 µg/mL), FFA-d3 18:0 (1 µg/mL), FFA-d3 16:0 (1 µg/mL), SM 12;0 (0.87 µg/mL), PE30;0 (0.92 µg/mL), PC 19:0 (1.12 µg/mL).</p>LipidIN: a comprehensive repository for flash platform-independent identification and reverse lipidomics.Xiamen UniversityXu Haoblood serummass spectrometry assay<p>We employed three distinct based liquid-liquid extraction methods to extract lipids from these sera samples. The lipid mixture data sets extracted from brown adipose tissue, brain, colon, heart, kidney, liver, lung, pancreas, soleus muscle, spleen, testis and white adipose tissues of mice, are based on methyl tert-butyl ether (MTBE) extraction method. The LC coupled with Orbitrap ID-X Tribrid mass spectrometric system was employed for lipidome analysis. The mobile phase A consists of acetonitrile and water (60:40, v/v) containing 10 mM NH4Ac, while mobile phase B consists of isopropyl alcohol and acetonitrile (90:10, v/v).</p>Homo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS10170Xu Hao. Xiamen University, Xiamen City, Fujian Province. 852152344@qq.com.<p>Raw data, regardless of its original format, undergoes conversion to the mzML format via MSConvert and subsequent quantization through XCMS. </p>CohortDisease852152344@qq.com<p>We have collected clinical data from three distinct cohorts. The first cohort includes 1,393 individuals, comprising 695 healthy volunteers and 698 breast cancer patients. The second independent cohort consists of 333 individuals, including 191 healthy volunteers and 142 breast cancer patients. The third cohort includes 105 individuals, with 31 cases of breast nodules, 32 cases of breast cancer without lung metastasis (referred to as breast cancer), 22 cases of breast cancer with lung metastasis, and 20 cases of female lung cancer. Serum samples from both breast cancer patients and healthy subjects were collected and stored at -80°C until analysis.</p><p><br></p><p>Written informed consent was obtained from each participant or from the participant’s parents or legal guardians in the discovery, and validation cohorts, and the study was conducted according to the Declaration of Helsinki. Ethical permission was granted by Xiamen University Ethics Committee, Fujian Province, China (Approval number: XDYX202302K08), and Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China (Approval number: 2022KY111).</p>Metabolomicslung cancerZenoTOF 7600ClinicalLipidomicsbreast canceruntargeted metabolite profilingPaternò–Büchi reactionlung cancerZenoTOF 7600ClinicalLipidomicsbreast canceruntargeted metabolite profilingPaternò–Büchi reaction<p>7600 EAD samples</p><p>For electron-activated dissociation (EAD) data acquisition, an Exion liquid chromatography (LC) coupled with a quadrupole time-of-flight MS system (ZenoTOF 7600, SCIEX, Framingham, MA, USA). Capilary voltage of 3500 V for positive.</p><p>Scan mode: MRMHR (Multiple Reaction Monitoring High Resolution) IS (Ion Source): 5500 GS1 (Gas Shield 1): 55 GS2 (Gas Shield 2): 55 TEM (Temperature): 550 CAD (Collision-Activated Dissociation): 9.</p><p>&nbsp;</p><p>P-B reaction samples</p><p>Electrospray ionization (ESI) was employed to detect positive ion modes. After separation by UPLC, the samples were analyzed using a Xevo G2-XS Q-TOF mass spectrometer (Waters). The ESI source conditions were as follows: Source Capillary (KV): 2.5; Sampling Cone: 40; Source Offset: 80; Source Temperatures: 120 °C; Desolvation Temperatures: 500 °C; Cone Gas Flows: 50 L/h; Desolvation Gas Flows: 800 L/h; MS1 scan ranges: 400-1000 m/z.</p><p>&nbsp;</p><p>105 case MS/MS samples</p><p>Data in both positive and negative ion modes were collected for all samples, with LC-MS and LC-MS/MS data collected simultaneously under each mode. The instrument was an Agilent 6546 Q-TOF Mass Spectrometer, with a Waters Acquity CSH C18 column, 1.7 µm. The scanning range was 150-1500 m/z. The MS/MS collision energy was 10-60 eV.</p><p>&nbsp;</p><p>335 case MS/MS samples</p><p>A Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (H-ESI) source. Capilary voltage of 3400 V for positive and 3000 V for negative. Data in both positive and negative ion modes were collected for all samples. Orbitrap mass analyzer operated at 120000 mass resolution was used in MS1 and 15000 mass resolution was used in MS2. The internal Mass Calibration remains on the whole time.</p><p>&nbsp;</p><p>1500 case MS/MS samples</p><p>A Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (H-ESI) source. Data acquisition was operated under alternating mode, with a capillary voltage of 3500 V for positive and 2400 V for negative. Orbitrap mass analyzer operated at 120000 mass resolution was used in MS1 and 15000 mass resolution was used in MS2. The internal Mass Calibration remains on the whole time.</p><p>&nbsp;</p>falseLipidIN: a comprehensive repository for flash platform-independent identification and reverse lipidomics<p>We present expeditious querying, reliable and platform-independent lipid annotation software LipidIN, a comprehensive lipidome atlas with tandem mass spectrometry information, relative retention time and reverse mass spectrometry information. Five-levels spectral fragmentations trees were formulates across 165.6 million lipids with Paternò − Büchi reaction and Electron activated dissociation included. Flash entropy search speeds up 69.65 billion times spectra querying in less than 1 s. Lipid categories intelligence models and reverse mass spectrometry information dramatically reduce false discoveries. Using 1833 clinical cohorts to demonstrate the reliability of lipidIN in clinical lipid investigations.</p>2025-03-212024-05-12MTBLS10170