Table 1.

Number of localizations by FP tagging for each of the 11 subcellular compartments in SUBA3.

Intracellular location	FP localizations	FP localizations confirmed by MS	FP localizations contradicted by MS	FP and MS localizations agree/disagree (% of proteins with both FP and MS data)	FP localizations neither confirmed nor contradicted
Cytoskeleton	63	0	24	0/100	39
Cytosol	514	119	101	54/46	294
ER	189	31	56	36/64	102
Extracellular	40	9	10	47/53	21
Golgi	145	42	57	42/58	46
Mitochondrion	312	90	54	63/37	168
Nucleus	779	95	149	39/61	535
Peroxisome	130	59	33	64/36	38
PM	245	122	17	88/12	106
Plastid	486	248	34	88/12	203
Vacuole	93	34	18	65/34	41
Total	2996	849	554	61/39	1593

Also shown are the numbers of FP localizations that overlap with MS localization and are thus confirmed by this approach, the numbers of FP localizations that disagree with MS localizations, the percentage of agreements and disagreements of FP with MS localizations for proteins for which FP tagging and proteomics data are both available, and the numbers of FP localizations that are neither confirmed nor contradicted by MS data. Data sets were extracted from the SUBA3 database (http://suba.plantenergy.uwa.edu.au).

Abbreviations: FP, fluorescent protein; MS, mass spectrometry; ER, endoplasmic reticulum; PM, plasma membrane.