Mass Spectrometry Data Processing Pipeline

SCIEX Analyst Workstation Software (Version 1.6.3) was employed for MRM data acquisition and processing. MS raw data (.wiff) files were converted to the .txt format using msConvert. The R program and database were applied for peak detection and annotation (Smith et al., 2006 (link); Kuhl et al., 2012 (link); Zhang et al., 2015 (link)). In the ion chromatogram, the target compounds showed symmetrical chromatographic peaks, and the chromatographic separation of the target compounds was well achieved. After data processing, orthogonal partial least squares-discriminant analysis (OPLS-DA) and principal component analysis were performed on metabolite data before and after inoculation, and the results were visualized by scatter plots (Mi et al., 2019 (link); Yang et al., 2020 (link)). Differentially accumulated metabolites (DAMs) between the pre-E. cristatum and post-E. cristatum groups were determined according to t-test value of p <0.05 and VIP >1. Lastly, the KEGG pathway database was used to enrich the metabolic pathways of DAMs, and R was used to visualize the results.