Figure 5: Protein profiles of serum-free EIAV-CMV-GFP, EIAV-CMV-COX2 and EIAV-CMV-tbsCOX2 vector preparations made in the presence of TRAP.

Quadruplicate serum-free vector concentrates were analysed by Mass Spectrometry Spectral Index-Normalized Quantitation (MS-SINQ). The profiles represent hits that varied by less than four-fold between replicate samples. EIAV-CMV-GFP and EIAV-CMV-COX2 represent ‘inert’ and ‘active’ transgene profiles respectively, compared to the ‘repressed’ transgene profile of EIAV-CMV-tbsCOX2. A large number of rare proteins were upregulated in EIAV-CMV-COX2 preparations (making up its profile ‘tail’), and to a lesser extent also in EIAV-GFP. Changes within the top ∼150 proteins (∼90% of total detected) in EIAV-CMV-COX2 were less pronounced, with the exception of Gag, VSV-G and Fibronectin, which were reduced and appeared at lowing rankings. Common hits were used in three-way comparison of peptide pools of quadruplicates of each vector type, summarized in Table 1.