## 3 Results  
### Identification of Cucurbita pepo Differentially Expressed Proteins  
The raw peptide sequences from all four sample groups, obtained via LC/MS-MS were mapped against protein fasta files, downloaded from NCBI and CuGenDB databases using the Proteome Discoverer 2.2 software package, resulting in 2070 annotations. After peptide identification, entries from both databases were matched against each other to determine common and unique entries. Nearly 9.5% (175) of CuGenDB entries lacked a corresponding annotation in NCBI. While the comparison of peptide descriptions did not show substantial differences between the two databases, 196 NCBI entries were labeled as \"uncharacterized proteins\" (Supplementary Table S1). Since CuGenDB had slightly more detailed annotations it was used in all downstream comparisons. Three experimental conditions were tested against controls (C) with empirical Bayes statistics through the DEP package in R; (a) plants inoculated with _P. xanthii_ conidia (PX vs. C), (b) RS sprayed plants (RS vs. C), and (c) RS sprayed plants inoculated with _P. xanthii_ conidia (RSPX vs. C). Additionally, three pairwise comparisons were performed between the treatments: RS vs. PX, RSPX vs. PX, and RSPX vs. RS. To gain insight into the test behavior across comparisons and decide the level of the significance thresholds, \(p\)-value histograms were created (Supplementary Figure S2). An anti-conservative pattern was revealed for the \(p\)-value distributions for the three treated samples, whereas the \(p\)-value distributions for the remaining three comparisons between treated samples appeared uniform. Based on the uniform part of the anti-conservative distributions, we adopted a \(p\)-value threshold of <0.05 combined with an absolute fold change of more than two, which is a commonly cited threshold in proteomics analyses [46, 48, 49, 50, 52, 53]. A summary of the differentially expressed proteins (DEPs) for a \(p\)-value \(<\) 0.05 and log2 fold change \(>\) 1 (absolute value for 2-fold change and above) is presented in Table 1. An elevated number of DEPs was observed in all three comparisons to the Control, with all other comparisons having four to five times less DEPs. The highest number of proteins exhibiting at least a 2-fold difference was found in the comparison of infected to control plants (PX vs. C), with 199 proteins in total, of which nearly two thirds were upregulated in the infected plants. Similar numbers for DEPs with differences above 2-fold were observed in the comparisons of RS-treated plants with and without infection versus the Control (comparisons RS vs. C and RSPX vs. C, respectively) with up- and down-regulated proteins ranging at similar orders of magnitudes in these comparisons. All relevant information regarding \(p\)-value significance and differential expression levels for all 2070 annotated proteins in all samples is provided in Supplementary Table S1. In Figure 1, a heatmap of the top 100 proteins with the highest fold in expression displays, in a visual way, various grouped DEPs in relation to the different treatments. The horizontal dendrogram shows a clear separation of the Control sample from all treated (PX, RS, and RSPX) samples, and a closer hierarchical relation of the RS and RSPX samples compared to PX. Moreover, a uniform intra-grouping (four sample replicates) for all different cases is observed. The vertical dendrogram presents clusters of DEPs with a similar pattern of expression along the four different cases. In clades 6 and 4, indicative groups of up- or down-regulated proteins irrespective of the treatments are shown to be clearly differentiated in all three treatments from the Control. In clades 5 and 1, examples of the effects of RS on the expression of indicative DEPs compared to all other sample groups, and its related effect also in the corresponding RSPX samples, are shown. Clades 2 and 3 indicatively show up- or down-regulated DEPs in PX samples compared to other treatments and the Control.