Table 1 Impact of the vProID score on the sensitivity and specificity of virus identification for various filtering strategies of peptide identification results

From: vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics

Filtering					Peptide identifications			Specificity						Sensitivity
Parameter set	vPro	FDR [%]	Min. CScore	Min. peptides (virus)	Peptides (human)	Peptides (virus)	Peptides (contaminants)	False positive virus tests	Total negative virus tests	Specificity (tests) [%]	False positive samples	Total negative samples	Specificity (samples) [%]	Correct positive samples	Total positive samples	Sensitivity [%]
1	No	1	0	1	805,681	2361	662	979	21,788	95,5	8	8	0	37	58	64
2				2	805,681	2361	662	136	21,788	99,4	8	8	0	33	58	57
3				3	805,681	2361	662	73	21,788	99,7	8	8	0	31	58	53
4				5	805,681	2361	662	68	21,788	99,7	8	8	0	21	58	36
5		0.1		1	527,111	357	434	88	21,788	99,6	4	8	50	34	58	59
6				2	527,111	357	434	32	21,788	99,9	2	8	75	30	58	52
7				3	527,111	357	434	12	21,788	99,9	0	8	100	25	58	43
8				5	527,111	357	434	0	21,788	100	0	8	100	14	58	24
9		1	0.95	1	686,735	888	558	314	21,788	98,6	7	8	13	37	58	64
10				2	686,735	888	558	63	21,788	99,7	7	8	13	32	58	55
11				3	686,735	888	558	56	21,788	99,7	5	8	38	29	58	50
12				5	686,735	888	558	40	21,788	99,8	2	8	75	19	58	33
13		0.1		1	527,111	357	434	88	21,788	99,6	4	8	50	34	58	59
14				2	527,111	357	434	32	21,788	99,9	2	8	75	30	58	52
15				3	527,111	357	434	12	21,788	99,9	0	8	100	25	58	43
16				5	527,111	357	434	0	21,788	100	0	8	100	14	58	24
1	Yes	1	0	1	805,681	2361	662	225	21,788	99,0	8	8	0	37	58	64
2				2	805,681	2361	662	13	21,788	99,9	3	8	63	33	58	57
3				3	805,681	2361	662	0	21,788	100	0	8	100	31	58	53
4				5	805,681	2361	662	0	21,788	100	0	8	100	21	58	36
5		0.1		1	527,111	357	434	59	21,788	99,7	2	8	75	34	58	59
6				2	527,111	357	434	0	21,788	100	0	8	100	30	58	52
7				3	527,111	357	434	0	21,788	100	0	8	100	25	58	43
8				5	527,111	357	434	0	21,788	100	0	8	100	14	58	24
9		1	0.95	1	686,735	888	558	94	21,788	99,6	3	8	63	37	58	64
10				2	686,735	888	558	0	21,788	100	0	8	100	32	58	55
11				3	686,735	888	558	0	21,788	100	0	8	100	29	58	50
12				5	686,735	888	558	0	21,788	100	0	8	100	19	58	33
13		0.1		1	527,111	357	434	59	21,788	99,7	2	8	75	34	58	59
14				2	527,111	357	434	0	21,788	100	0	8	100	30	58	52
15				3	527,111	357	434	0	21,788	100	0	8	100	25	58	43
16				5	527,111	357	434	0	21,788	100	0	8	100	14	58	24

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Table 1 Impact of the vProID score on the sensitivity and specificity of virus identification for various filtering strategies of peptide identification results

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