Enrichment of PM from potato roots
PM enrichment was critical for the subsequent membrane proteome analysis. The effectiveness of the two-phase partitioning PM enrichment method was evaluated immunologically using compartment-specific antibody markers (Fig. 1). The abundance of the PM marker H+-ATPase was 13.3-fold higher in the PM fraction compared to the original crude extract (CE), and three-fold higher than in the microsomal (M) fraction (Supplementary Fig. S3). In contrast, both the cytosolic marker MDAR (highly abundant in the soluble phase (S)) and the mitochondrial marker VDAC (highly abundant in the microsomal and the lower phase Dextran T500 phase (M and LP)), were barely detectable in the upper PM-enriched phase (PMe). BiP was represented in the PM fraction, but to an intensity three-fold lower than in the M fraction. V-type ATPase was present at a comparable levels in the M, LP and PMe fractions. These results indicate that the PM proteins were enriched in the upper phase, which was used in our comparative proteome analysis.