Table II. Overview of the acquired proteomics data. Experimental details of the quantitative data presented per SCX-LC-MS/MS experiment. Protein and peptide numbers are based on the included spectra after filtering to a false discovery rate (FDR) of 1%. Numbers are either redundant (r) or nonredundant (nr).

	LV-mouse 1/SILAC	RV-mouse 1/SILAC	LV-mouse 2/SILAC	RV-mouse 2/SILAC
Number of SCX fractions analyzed	28	25	25	25
MS/MS Spectra	335064	269237	524573	453597
FDR Mascot Score Threshold CID	23.8	24.4	26.9	27.6
FDR Mascot Score Threshold ETD	23.6	23.9	23.7	25.7
Identified Spectra within 1% FDR (% of total)	42975 (13%)	33944 (13%)	70354 (13%)	58716 (13%)
CID spectra (FDR1%) (r)	24204	18617	33484	27338
ETD spectra (FDR1%) (r)	18771	15327	36870	31378
Unique Peptides (FDR 1%) (nr)	14357	11473	14941	13754
Unique Peptides Identified in all 4 experiments (r)	28115
Unique Peptides CID (FDR 1%) (nr)	11839	9430	10244	8758
Unique Peptides ETD (FDR 1%) (nr)	9128	7634	11634	10680
Proteins Identified	2176	1823	2324	2180
Proteins Identified over all 4 experiments (nr)	3749
Quantitated Peptide Pairs (r)	22849	17400	35928	30849
Quantitated Proteins (nr)	1899	1611	1971	1904
Quantitated proteins over all 4 samples (nr)	3107
Average (median) quantitated peptides/protein	12 (3)	11 (3)	18 (4)	16 (3)
Proteins quantitated in both LV and RV	1303		1457
Proteins quantitated in each of the 4 samples	906