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 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...
| Autores: | , , , , , , |
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| Tipo de recurso: | conjunto de datos |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/369434 |
| Acceso en línea: | http://hdl.handle.net/10261/369434 https://doi.org/10.20350/digitalCSIC/16601 |
| Access Level: | acceso abierto |
| Palabra clave: | Resistance Endophyte Untargeted metabolomics LC-MS Zea mays Maize Fusarium verticillioides Sesamia nonagrioides endophytes maize |
| Sumario: | [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 > 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) > 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. |
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