Mascot *.dat files were created in Mascot and loaded into Scaffold (version 3_00_05). Peptide and protein probabilities were calculated using PeptideProphet and ProteinProphet algorithms [90] . We reported protein accession numbers that could be identified on the basis of at least one peptide with a Mascot score exceeding the identity threshold and E-value ,0.05. The FDR was less than 1.0%. Spectral counts were normalized to the total and compared between treated and non-treated virions, as well as a healthy control. The healthy control consisted of the fraction in the sucrose gradient corresponding to the virus sedimentation position. Proteins were not reported if they were also detected in the healthy control (Table S1 ). To minimize redundancy due to effects of homology-based searching, only one protein per protein family were reported. Rubisco was abundant in all virus and healthy plant samples.