Fig. 2: Proteomic analysis of the Arabidopsis leaf APF.

Total protein from the clarified CL and the APF were trypsinized and subjected to LS-MS/MS. Individual proteins were identified by Proteome Discover whose abundances were then determined semi-quantitatively based on the combined ion intensities determined from the MS1-scans (e-values). The CL and APF were each assayed by four biological replicates each measured with two technical replicates; protein abundances were then normalized based on the total MS1 ion intensities for all proteins in each. Only those proteins detected in at least one technical replicate for each of the four biological replicates were included. Values for the Rubisco large and small subunits were removed from the APF prior to analysis to avoid their abundance bias. a Pie charts showing the percentage of proteins localized to specific compartments/complexes in the APF versus CL using assignments either provided by GO or from a master list of apoplastic proteins (See Supplementary Data 5). ER endoplasmic reticulum. PM plasma membrane. b Volcano plots of 1156 proteins found in both the CL and APF showing their relative abundances based on their MS1 ion intensities. Green and orange points identify chloroplast and apoplast proteins, respectively. All others are colored in grey. The numbers of proteins with significant or insignificant differences in abundance between CL and APF are indicated in the corners of the graphs. The dashed lines indicate the significance boundaries based on both Log₂ FC ≥1 or ≥-1 and P-value of significance <0.05. c Functional analysis of the CL (2921 total), APF (1375 total), and APF-specific proteins (219 total) as determined by GO. Shown are the top 5-6 GO terms for each set based on the Cellular Compartment, Biological Process, and Molecular Function categories. Top left, Venn diagram showing the overlap of the two fractions.