MetaboLights

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intensity of peak data was further preprocessed by metaX. Those features that were detected in less than 50% of QC samples or 80% of biological samples were removed, the remaining peaks with missing values were imputed with the k-nearest neighbor algorithm to further improve the data quality. PCA was performed for outlier detection and batch effects evaluation using the pre-processed dataset. Probabilistic Quotient Normalization (PQN) was used to normalize the data to obtain the normalized ion intensity data of each sample. Quality control-based robust LOESS signal correction was fitted to the QC data with respect to the order of injection to minimize signal intensity drift over time. In addition, the coefficient of Variation (CV) of the metabolic features were calculated across all QC samples, and those > 30% were then removed.MetaboLightsPublicLiquid Chromatography MS - negative - reverse phaseLiquid Chromatography MS - positive - reverse phaseFirst group samples to ensure that different groups are cross-sorted on the machine, all samples were acquired by the LC-MS system followed machine orders. All chromatographic separations were performed using a Thermo Scientific UltiMate 3000 HPLC. An ACQUITY UPLC T3 column (100 mm x 2.1 mm, 1.8 µm, Waters, UK) was used for reversed-phase separation. The column oven was maintained at 50 °C. The flow rate is 0.3 mL/min, and the mobile phase consists of phase A (water, 0.1% formic acid) and phase B (acetonitrile, 0.1% formic acid). Gradient elution conditions were set as follows: 0.0-0.8 min, 2% B; 0.8-2.8 min, 2-70% B; 2.8-5.6 min, 70-90% B; 5.6-8.0 min, 90-100% B;8.0-8.1 min, 100-2% B; 8.1-10.0 min, 2% B. The injection volume for each sample was 4 µL. First scan one or two WASH samples, followed by 3-4 Comprehensive analysis of the microbiome and metabolome in pus from pyogenic liver abscess patients with and without diabetes mellitus.Yawen GuoDepartment of Radiology, Shengjing Hospital of China Medical University, Shenyang, Chinalivermass spectrometry assayThe collected samples were thawed on ice; add 500 μL precooled 80% methanol to 1.5mL EP tube; 50 mg sample was added to the tube and homogenized; the extraction mixture was then stored at -20 °C for 2 h; after centrifugation at 20,000 x g for 10 min, the supernatants were transferred into new 1.5 mL EP tube and dried; the dried extract was stored at -80 °C; reconstitute the dried extract in 100 μL precooled 80% methanol, take an equal part of each sample as pooled QC sample.Homo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS7128Yawen Guo. China Medical University. No.36 Sanhao Street, Heping District Shenyang, Liaoning. 275766769@qq.com.Import the acquired mass spectrum raw data (.raw files) into Compound Discoverer 3.1.0 (Thermo Fisher Scientific, USA) for data pretreatments, including: peak extraction, retention time correction within and between groups, adduct ion merging , fill gaps, background peak labeling and metabolite identification. Each ion was identified by combining retention time (RT) and m/z data. Intensities of each peaks were recorded and finally export information such as feature molecular weight, retention time, peak area and identification results.The online KEGG, HMDB database was used to annotate the metabolites by matching the exact molecular mass data, name and formula of samples with those from database. If a mass difference between observed and the database value was less than 10 ppm, the metabolite would be annotated.Disease275766769@qq.comThe characteristics of lesions (size, location, liquefaction, separation) were assessed according to the preoperative CT. The 5F puncture needle was punctured into the abscess cavity using Seldinger technique with real-time visualization of sonographic. Finally, 8F pig tail multi-use drainage catheter was introduced into the cavity using Trocar technique under the guidance of fuoroscopy (Two-Step Centesis catheter). For patients with liver abscesses with viscous pus, a larger caliber of catheter would be recommended to insert into the abscess cavity. Technical success was defned as the pig tail of catheter inserted into the cavity with free aspiration of pus and the lateral orifces of catheter completely within the cavity. According to our center’s practice, the removal criteria of catheter were defned as the drainage volume of pus less than 5 mL over 3 consecutive days, improvement in the patient’s clinical symptoms such as fever, decreased white cell count if they had leukocytosis before the drainage. Metabolomicsultra-performance liquid chromatography-mass spectrometryLiver Abscesstandem mass spectrometry16S rRNA sequencinguntargeted metabolitesultra-performance liquid chromatography-mass spectrometryLiver Abscesstandem mass spectrometry16S rRNA sequencinguntargeted metabolitesA high-resolution tandem mass spectrometer Q-Exactive (Thermo Scientific) was used to collect first and secondary order spectrum data of the metabolites eluted form the column. The Q-Exactive was operated in both positive and negative ion modes. Precursor spectra (70-1050 m/z) were collected at 70,000 resolution to hit an AGC target of 3e^6. The maximum inject time was set to 100 ms. A top 3 configuration to acquire data was set in DDA mode. Fragment spectra were collected at 17,500 resolution to hit an AGC target of 1e^5 with a maximum inject time of 50 ms.Fragmentation energy (stepped nce) is set as: 20, 40, 60 eV. Ion source (ESI) parameter settings: spray voltage (|KV|)) was 4000 (positive) and 4000 (negative), Sheath gas flow rate was 35, Aux gas flow rate was 10, Capillary temperature was 320 °C.falseComprehensive analysis of the microbiome and metabolome in pus from pyogenic liver abscess patients with and without diabetes mellitusPyogenic liver abscess (PLA) patients combined with diabetes mellitus (DM) tend to have more severe clinical manifestations than without DM. The mechanism responsible for this phenomenon is not entirely clear. The current study therefore aimed to comprehensively analyze the microbiome composition and metabolome in pus from PLA patients with and without DM, to determine the potential reasons for these differences. Clinical data from 290 PLA patients were collected retrospectively. We analyzed the pus microbiota using 16S rDNA sequencing in 62 PLA patients. In addition, the pus metabolomes of 38 pus samples were characterized by untargeted metabolomics analysis. Correlation analyses of microbiota, metabolites and laboratory findings were performed to identify significant associations. PLA patients with DM had more severe clinical manifestations than PLA patients without DM. There were 17 discriminating genera between the two groups at the genus level, among which Klebsiella was the most discriminating taxa. The ABC transporter was the most significant differential metabolic pathway predicted by PICRUSt2. Untargeted metabolomics analysis showed that concentrations of various metabolites were significantly different between the two groups, and seven metabolites were enriched in the ABC transporter pathway. Phosphoric acid, taurine and orthophosphate in the ABC transporter pathway were negatively correlated with the abundance of Klebsiella and the blood glucose level. The results showed that the abundance of Klebsiella in the pus cavity of PLA patients with DM was higher than those without DM, accompanied by changes of various metabolites and metabolic pathways, which may be associated with more severe clinical manifestations. 2026-01-242023-02-13MTBLS7128