Table III.

Confirmation and contradiction apparent between FP- and MS-based experimental subcellular localization data in the four major cellular compartments (mitochondria, plastids, nucleus, and PM)

MS Data, The number of confirmations of MS data for the four compartments by the FP and SP data are shown; below each confirmation are the number of proteins in the FP and SP sets that are present in the MS sets for each location, but the FP and SP localization data contradict the MS data by suggesting a different location in the cell. The percentages shown in parentheses show the percentage of the total numbers in the relevant MS datasets for each organelle. FP Data, The number of confirmations of FP data for the four compartments by MS and SP data are shown; below each confirmation are the number of proteins in the MS and SP sets that are present in the FP sets, but the MS and SP localization data contradict the FP data. The percentages shown in parentheses show the percentage of the total numbers in the relevant FP datasets for each organelle. FP, Fluorescent protein-derived set; MS, mass spectrometry proteomics-derived set; SP, Swiss-Prot database-derived set.

MitoPlastidNucPM
MS DataMS-Mito (547)MS-Plastid (1,017)MS-Nuc (367)MS-PM (534)
    Confirmed by FP16 (3%)23 (2%)75 (20%)19 (4%)
    Contradicted by FP17 (4%)44 (4%)10 (3%)33 (6%)
    Confirmed by SP99 (18%)173 (17%)18 (4.9%)44 (8%)
    Contradicted by SP33 (6%)71 (7%)46 (13%)47 (9%)
FP DataFP-Mito (73)FP-Plastid (118)FP-Nuc (320)FP-PM (84)
    Confirmed by MS16 (22%)23 (19%)75 (23%)18 (21%)
    Contradicted by MS7 (10%)8 (7%)16 (5%)5 (6%)
    Confirmed by SP11 (15%)30 (25%)50 (16%)7 (8%)
    Contradicted by SP7 (10%)1 (1%)17 (5%)8 (10%)