The identification of metabolites is a combined result of BMDB database, mzCloud and ChemSpider (HMDB, KEGG) databases. Main parameters of metabolite identification: Precursor Mass Tolerance < 5 ppm, Fragment Mass Tolerance < 10 ppm, RT Tolerance < 0.2 min. The results of the Compound Discoverer 3.1 export are imported into metaX for data preprocessing, including: 1. Normalize the data using the Probabilistic Quotient Normalization (PQN) (Di Guida et al. 2016) to obtain the relative peak area. 2. Correct the batch effect using QC-RLSC (Quality control-based robust LOESS signal correction) (Dunn et al. 2011); 3. Calculate the CV (Coefficient of Variation) of the relative peak area in all QC samples, and delete the compounds with CV greater than 30%.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - positive","Liquid Chromatography MS - negative"],"chromatography_protocol":["The Waters 2D UPLC (Waters, USA) coupled with a Q Exactive high-resolution mass spectrometer (Thermo Fisher Scientific, USA) was used for metabolite separation and detection. The chromatographic column used was a BEH C18 column (Waters, USA). The mobile phases for positive ion mode were water with 0.1% formic acid (A) and methanol with 0.1% formic acid (B); for negative ion mode, water with 10 mM ammonium formate (A) and 95% methanol with 10 mM ammonium formate (B). The gradient elution was as follows: 0.0-1.0 min, 2% B; 1.0-9.0 min, 2-98% B; 9.0-12.0 min, 98% B; 12.0-12.1 min, 98-2% B; 12.1-15.0 min, 2% B. The flow rate was 0.35 mL/min, the column temperature was 45 °C and the injection volume was 5 μL.
"],"publication":["Poultry Science, frontiers in veterinary science."],"submitter_name":["Wei Xiaona"],"submitter_affiliation":["Zhengzhou University"],"organism_part":["blood plasma"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["After thawing at 4 °C, 100 μL of each sample was placed in a 96-well plate. Subsequently, 300 μL of extraction reagent (methanol:acetonitrile:water, 2:2:1, v:v:v) and 10 μL of internal standard were added. The mixture was vortexed for 1 min and left to stand at -20 °C for 2 h. Samples were then centrifuged at 4 °C, 4000 rpm for 20 min. And 300 μL of each supernatant were transferred to a freeze-drying concentrator and dried. The residues were reconstituted with 150 μL of reconstitution reagent (methanol:H2O, 1:1, v: v), vortexed for 1 min, centrifuged at 4 °C, 4000 rpm for 30 min, and each supernatant were transferred to sample vials. A pooled QC sample was prepared by combining 10 μL of supernatant from each sample to evaluate the reproducibility and stability of the LC-MS analysis.
"],"organism":["Gallus gallus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS11832"],"author":["Xiaona Wei. weixn@zzu.edu.cn. +8618011900838."],"data_transformation_protocol":["The mass spectrometry raw data (raw file) collected by LC-MS/MS was imported into Compound Discoverer 3.1 (Thermo Fisher Scientific, USA) for data processing, including: peak extraction, retention time correction within and between groups, additive ion pooling, missing value filling, background peak labeling and metabolite identification, and finally information on compound molecular weight, retention time, peak area and identification results were exported.
"],"study_factor":["Infection"],"submitter_email":["weixn@zzu.edu.cn"],"sample_collection_protocol":["Briefly, 27 4-week-old SPF chickens were randomly divided into 3 groups, 9 birds each group. Chickens in one group were inoculated with 0.5 mL medium by intramuscular injection into the leg as negative control, and chickens in the other 2 groups were inoculated with 0.5 mL x 108 CCU/mL of ZX313 strain and SD2 strain respectively. At 2 weeks post infection (wpi.), the live chickens were humanely euthanized and necropsied while plasma samples from each group were collected and stored at -80 °C for subsequent untargeted metabolomics analysis.
"],"omics_type":["Metabolomics"],"study_design":["untargeted metabolites","Mycoplasma synoviae","Virulence Factors"],"curator_keywords":["untargeted metabolites","Mycoplasma synoviae","Virulence Factors"],"mass_spectrometry_protocol":["The Q Exactive mass spectrometer was used for primary and secondary mass spectrometry data acquisition. The full scan range was 70-1050 m/z with a resolution of 70,000, AGC (automatic gain control) target of 3e6, and maximum injection time of 100 ms. The top 3 precursors were selected for subsequent fragmentation with a resolution of 17,500, AGC target of 1e5, maximum injection time of 50 ms, and stepped nce of 20, 40, 60 eV. ESI parameters were: sheath gas flow rate 40, auxiliary gas flow rate 10, spray voltage 3.80 kV for positive mode and 3.20 kV for negative mode, capillary temperature 320 °C and auxiliary gas heater temperature 350 °C.
"],"additional_accession":[]},"is_claimable":false,"name":"Metabolomics reveals plasma profiles of Mycoplasma synovise infection with different virulence","description":"Mycoplasma synovise (MS) is a prominent pathogen of poultry, causing considerable economic pressure to the poultry industry. Although we have a basic understanding of MS infection, the research on the pathogenicity and interactions between host and MS especially the metabolic bases of MS infection are still unclear. In this study, untargeted metabolomics analyses were conducted on plasma of SPF chickens infected with different virulence MS strains ZX313 and SD2. A total of 801 and 834 significant different metabolites (SDMs) were observed in ZX313 and SD2 infected samples respectively, among which 195 and 228 metabolites were group specific. Metabolic pathway enrichment analysis showed that MS infection disrupted amino acid metabolism, nucleotide metabolism and lipid metabolism of host. Moreover, tryptophan metabolites and fatty acid metabolites, differentially expressed in different virulence group, may related to the severity of the disease and the pathogenicity of MS. These findings may offer new insights into pathogenesis of MS and host-MS interaction.
","dates":{"publication":"2025-01-13","submission":"2024-12-03"},"accession":"MTBLS11832","cross_references":{}}