Table II. Comparison of major compartment assignments from Expts A and B.

Expt A, Highest Classification	# proteins with at least 2 peptides and 3 spectra meeting threshold				No threshold				(A∩B)/|A|
					≥0.5 classifier point estimate
					≥0.5 classifier lower confidence limit
					≥0.7 classifier point estimate
					≥0.7 classifier lower confidence limit
	Expt B, Highest Classification
	Mito	Ly/Per	ER	Golgi	PM	Cyto	Nuc	ALL
Mito	463	9	1			2		475	97.5%
	414	1	1			1		417	99.3%
	397							397	100.0%
	303							303	100.0%
	269							269	100.0%
Lyso	2	200	23	5	2	10		242	82.6%
	2	171	7	1	1	3		185	92.4%
	1	159	4			2		166	95.8%
	1	118						119	99.2%
		105						105	100.0%
Perox	4	75	1		1	1		82	91.5%
		67						67	100.0%
		60						60	100.0%
		31						31	100.0%
		27						27	100.0%
ER	7	11	440	49	25	6	1	539	81.6%
	1	1	376	11	7			396	94.9%
			320	1	4			325	98.5%
			243		1			244	99.6%
			198					198	100.0%
Golgi		7	18	88	9			122	72.1%
			6	49	3			58	84.5%
			1	36	2			39	92.3%
			1	15				16	93.8%
				12				12	100.0%
PM	6	21	17	10	222	7	1	284	78.2%
		3	6	1	159			169	94.1%
		1	3		126			130	96.9%
					58			58	100.0%
					30			30	100.0%
Cytosol	3	54	21	66	70	851	12	1077	79.0%
		16	5	14	12	720	1	768	93.8%
		11	3	9	5	676	1	705	95.9%
						484		484	100.0%
						433		433	100.0%
Nucleus		1		4	30	2	94	131	71.8%
					4	1	68	73	93.2%
					1	1	53	55	96.4%
							22	22	100.0%
							20	20	100.0%
ALL	485	378	521	222	359	879	108	2952	82.4%
	417	259	401	76	186	725	69	2133	94.9%
	398	231	331	46	138	679	54	1877	97.3%
	304	149	244	15	59	484	22	1277	99.8%
	269	132	198	12	30	433	20	1094	100.0%
(A∩B)/|B|	95.5%	72.8%	84.5%	39.6%	61.8%	96.8%	87.0%	82.4%
	99.3%	91.9%	93.8%	64.5%	85.5%	99.3%	98.6%	94.9%
	99.7%	94.8%	96.7%	78.3%	91.3%	99.6%	98.1%	97.3%
	99.7%	100.0%	99.6%	100.0%	98.3%	100.0%	100.0%	99.8%
	100.0%	100.0%	100.0%	100.0%	100.0%	100.0%	100.0%	100.0%