DOI: 10.20350/digitalcsic/16601
title: LC-MS dataset for the paper “Gesteiro, N.; Cao, A.; Santiago, R.; Lobagueira, P.; González-Prieto, S.J.; Malvar, R. A.; Butrón, A. Effects of seed infection by Fusarium verticillioides on maize performance against Sesamia nonagrioides attack. Physiologia Plantarum

description: [Description of methods used for collection/generation of data] Stem pith tissue samples were extracted with 80% methanol and filtered through a 0.22 µm PTFE membrane to an Eppendorf tube. An aliquot was transferred to a HPLC certified vial. Balanced pools of the total sample extracts were prepared as quality control (QC). Blank extractions were used. All samples were evaporated to dryness, stored at 4° C until analysis, and then dissolved in 80% methanol. Metabolomics profiles were acquired using an ultra‐high‐performance liquid chromatography (UHPLC) system (Thermo Dionex Ultimate 3000 LC) coupled to a quadrupole-time-of-flight mass spectrometer (QTOF-MS) equipped with an electrospray ionization source (ESI) (Bruker Compact; Bruker Daltonics). We measured the analytical samples using three analytical batches, each one con-taining 6 blocks of 10 analytical samples. The analytical samples were randomly assigned to batches and blocks within batches. Blanks were placed at the initial and final positions of each batch and QC samples were evenly distributed bordering the blocks. UHPLC separation was performed with a Inten-sity Solo 2 C18 column (1.7 µm, 2.1× 100 mm; Bruker Daltonics) in gradient elution consisted of 0.1% of formic acid on water (solvent A) and acetonitrile (solvent B) as mobile phase in a 0.4 ml/min flow rate. The elution conditions were: 0 min, 3 % B; 4 min, 3 % B; 16 min, 25 % B; 25min, 80% B; 30 min, 100% B; 32 min, 100% B; and return to initial conditions at 33 min (3% B) for 3 min. Full scan MS data were acquired in both positive and negative ionization modes over the mass range of 100–1200 m/z, and under the following specific conditions: gas flow 9 L min−1; nebuliser pressure 2.6 bar; dry gas 9 L min−1; dry temperature 220 °C. Auto MS/MS fragmentation was performed in pooled samples to facilitate compound identification. After each batch, the MS ion source was cleaned, and the MS was recalibrated. [Methods for processing the data:] We pre-processed the raw MS spectra using the algorithm T-Rex 3D in MetaboScape 4.0 software (Bruker Daltoniks, Germany). Parameters were set to separate measured peaks from background noise and features were grouped across samples and corrected for retention time shifts. After this pre-processing, data were prepared for statistical analysis using Metaboanalyst (Chong et al. 2019). Fea-tures with &gt; 75 % missing data were eliminated and missing data imputation was performed using the KNN (feature-wise) method. Afterwards ANCOVA method was used for batch correction and contam-inants present in blanks were removed. Features with percent relative standard deviation (RSD = SD/mean) &gt; 25 % across QCs samples were removed, as well as uninformative features that presented near-constant values detected by the interquartile range filter (IQR). Then, Pareto scaling was applied to adjust for the disparities in fold differences between the analytes.
description: This dataset belongs to an untargeted metabolomic study to investigate i) the responses in maize pith to the attack of the insect Sesamia nonagrioides under plant colonization by the fungus Fusarium verticillioides; ii) if the response differences could depend on genotype resistance to Fusarium; and iii) to determine metabolites associated to beneficial/detrimental changes of on maize performance. The dataset are LC-MS experimental data for untargeted metabolomics of pith tissues extracts from 8 maize inbred lines genetically diverse with different level of resistance to F. verticillioides infection. Inbred lines were PB130, EP77, A509, EP125, EP42, A637, A630, A239. Experimental treatments were four and labeled as: - Control-Control (CC): no seed inoculation with F. verticillioides and no infestation with S. nonagrioides; - Fusarium-Control (FC): seed inoculation with F. verticillioides and no infestation with S. nonagrioides; - Fusarium-Sesamia (FS): seed inoculation with F. verticillioides and plant infestation with S. nonagrioides; - Control-Sesamia (CS): no seed inoculation with F. verticillioides and plant infestation with S. nonagrioides. Up to six plant per genotype-treatment combination were used as biological replicates. Because of the large number of analytical samples were grouped in 3 analytical batches for LC-MS analyses. Each batch contains 6 blocks of 10 analytical samples. The analytical samples were randomly assigned to batches and blocks within batches. Blanks were placed at the initial and final positions of each batch and QC samples were evenly distributed bordering blocks. QCs were balanced pools of the total sample extracts. Spectral data were acquired in a LC-ESI-QTOF mass spectrometer (Bruker Daltonics). MS acquisition was performed in both negative and positive ionization modes for full scan in a mass scan range of m/z 100-1200 with Bruker OTOF Control and DataAnalisys software (Bruker Daltonics).The dataset raw data were converted to mzML format with ProteoWizard MSConvert tool (Version: 3.0.24261). Biosynthesis of unsaturated fatty acids and linolenic acid metabolism were downregulated in susceptible inbreds under the FS treatment compared to CS treatment, and glutathione metabolism and aminoacyl-tRNA biosynthesis upregulated. Phenylalanine, tyrosine and tryptophan biosynthesis (PTTB) pathway was enriched in the comparison FS versus CS in resistant inbreds, as well as other pathways highly related with PTTB pathway such as isoquinoline alkaloid biosynthesis and ubiquinone and other-terpenoid-quinone biosynthesis pathways.
description: File List: MS NEG Batch 1.zip MS NEG Batch 2.zip MS NEG Batch 3.zip MS POS Batch 1.zip.001 MS POS Batch 1.zip.002 MS POS Batch 1.zip.003 MS POS Batch 2.zip.001 MS POS Batch 2.zip.002 MS POS Batch 3.zip.001 MS POS Batch 3.zip.002