Skip to main content

Table 2 Comparison of deduced protein localization for the 254 co-isolating proteins, proteins detected by one unique peptide, and sporadically identified proteins

From: Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins

Locationa Co-isolating proteinsb “1 unique peptide” proteinsc “Sporadically identified” proteinsd
# proteins % % total proteins identified # proteins % % total proteins identified # proteins % % total proteins identified
Cytosol 92 36.22 4.21 59 34.10 2.70 52 36.11 2.38
Endomembrane 45 17.72 2.06 25 14.45 1.14 27 18.75 1.24
Mitochondrion 52 20.47 2.38 25 14.45 1.14 21 14.58 0.96
Nucleus 37 14.57 1.69 32 18.50 1.46 30 20.83 1.37
Peroxisome 19 7.48 0.87 5 2.89 0.23 4 2.78 0.18
Plasma membrane 4 1.57 0.18 9 5.20 0.41 1 0.69 0.05
Unknown/Multiple 5 1.97 0.23 17 9.83 0.78 9 6.25 0.41
Total 254 100.00 11.62 172 99.42 7.87 144 100.00 6.59
  1. aBased on predictions for the localization of the the tomato proteins by TargetP, ChloroP, Predotar, WoLF PSORT, and YLoc and the known localization (PPDB, plprot, SUBA4) and functions of Arabidopsis homologs proteins (TAIR); the locations of some proteins had multiple subcellular locations or their location could not be inferred
  2. bThe identity and putative locations of the proteins that reproducibly co-isolated (CIPs) with the tomato chloroplast stroma are found in Additional file 5: Table S5
  3. cThe identity and putative locations of the proteins identified by a single unique peptide are found in Additional file 3: Table S3
  4. dThe identity and putative locations of the proteins that were sporadically identified in the chloroplast stroma are found in Additional file 4: Table S4