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Pipeline publication

[…] 8 column (Sigma-Aldrich, ODS-2, 5 um, 4.6 × 250 mm). The method includes the use of water containing 1% acetic acid (phase A) and acetonitrile containing 1% acetic acid (phase B) with the following gradient: for three minutes, 3% of B, followed by a gradient of 3–12% of B for 25 min, 12–16% of B for 20 min, and 16–100% of B for three minutes. The column was washed and restabilized for seven minutes before the next injection. The flow used was 1 mL/min. All samples were injected in a random order and the same concentration of 1 mg/mL. MS spectra were acquired in positive mode and for the metabolomic analysis; the mass signals obtained from raw data files were extracted and aligned within the metAlign software program, with a final alignment of 5592 mass signals. Subsequently, the signals belonging to the same molecules, isotopes, fragments, and adducts, were regrouped using the MSClust software, resulting in 67 reconstructed metabolites. The molecular formulas of the major compounds were determined by peaks obtained by the mass spectrometer, taking into account the elements C, H, O, and N, the error being equal to or less than 5 ppm. The UV spectrum also characterized the compounds. Catechin and quercetin were identified through comparison with the authenticity standard (Sigma). Finally, the data was analyzed in Metaboanalyst 3.0 platform using Principal Component Analysis (PCA) and Heatmap. For PCA, data was log average transformed. For Heatmap, dispersion profile of the compounds and hierarchical clustering was organized using Euclidean distance, Ward clustering algorithm, and the top 40 metabolites selected by ANOVA (p ≤ 0.05)., The methodology was in accordance with the United States Pharmacopeia [] with minor modifications. Enrichment broths and selective media were used to research the viable microorganism count as well as for the identification of Salmonella sp., Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans []. Every procedure was carried out aseptical […]

Pipeline specifications

Software tools MetAlign, MSClust, MetaboAnalyst