The candidate host proteins considered for SRM studies included all of the proteins listed in Table 4 that were found to be exclusively associated with transmissible virus. Proteins found in both transmissible and non-transmissible virus were also considered since they may be found in different amounts in the aphid. All of these plant proteins were checked for similarity against all available aphid and aphid bacterial endosymbiont protein sequences. Peptides from proteins that were identical to aphid or endosymbiont proteins at the amino acid level were not considered for further analysis as only peptides unique to the plant proteins could be informative for the specific measurements of the plant proteins in aphids. Those that remained included cellulose synthase, thaumatin-like protein 5, 33-kD secretory protein, pyruvate dehydrogenase E1, pyruvate dehydrogenase E2, remorin, cysteine-rich repeat secretory protein 55-like, structural maintenance of chromosomes protein 3, and predicted ribosomal protein. We also included b-D-glucosidase which was abundant in healthy controls as well as the purified virus preparations. To perform relative quantification of these proteins, a method was created in Skyline [32] that identified peptides specific to each of the candidate virus-interacting host proteins and exported to a TSQ Vantage mass spectrometer operating in SRM mode. Total protein extracted from the efficient RPV-vector aphid species Rhopalosiphum padi (all developmental stages) fed on healthy or infected plants for 21 days was digested with trypsin and analyzed by SRM. Peptides from five of the plant proteins listed in Table 4 Figure 3. Effect of sodium sulfite and EDTA on CYDV-RPV virion (arrowhead) attachment to apical plasmalemma and endocytosis into the HG cells of R. padi following membrane acquisition. (A and B) no sulfite or EDTA (buffer only) virus is internalized into cells of R. padi HG and can be found in tubular vesicles; (C and D) EDTA only treatment shows no effect of EDTA on acquisition of virions into the aphid HG which is consistent with the transmission data presented in Tables 1 & 2 ; (E-F) sodium sulfite treatment prevents attachment and acquisition of virus into cells of the HG. APL, apical plasmalemma; HG, HG; L, lumen; TV, tubular vesicle; T, tubule; R, ribosome. doi:10.1371/journal.pone.0048177.g003 Table 3 . Effects of EDTA and sodium sulfite on R. padi transmission of purified cereal yellow dwarf virus-RPV using microinjection into the aphid hemolymph. [90] . Each unique peptide match is based on at least 2 distinct spectra, but in some cases, many more. In the case of cysteine-rich repeat secretory protein 55-like, more than 300 total spectra were matched, highlighting the limitations of a homology-based search strategy for protein identification [79] . doi:10.1371/journal.pone.0048177.t004