Table 2.

The capability of the identified amyloid signature proteins, and combinations of these, to discriminate amyloid-containing biopsies from CR-negative samples. Support Vector Machine algorithm was developed based on the quantitative readout (number of peptide spectrum matches) of each of the identified amyloid signature protein (Table 1) from the proteomics analysis of the biopsies from the training set. The test data set consisted of 22 amyloid-containing biopsies (“+”) and 23 corresponding controls without amyloid (“−”).

Signature Protein (s)	Correct/Total	Sensitivity	Specificity	PPV	NPV	Accuracy
ApoA4	+: 21/22 −: 22/23	0.95	0.96	0.95	0.96	0.96
ApoE	+: 22/22 −: 22/23	1.00	0.96	0.96	1.00	0.98
SAP	+: 21/22 −: 23/23	0.95	1.00	1.00	0.96	0.98
Clusterin	+: 20/22 −: 23/23	0.90	1.00	1.00	0.92	0.96
Vitronectin	+: 6/22 −: 23/23	0.27	1.00	1.00	0.59	0.64
Complement C9	+: 2/22 −: 23/23	0.09	1.00	1.00	0.53	0.56
Collagen alpha-1(VI) chain	+: 14/22 −: 21/23	0.64	0.91	0.88	0.72	0.78
Collagen alpha-2(VI) chain	+: 13/22 −: 20/23	0.59	0.87	0.81	0.69	0.73
Collagen alpha-3(VI) chain	+: 13/22 −: 20/23	0.59	0.87	0.81	0.69	0.73
Fibulin-1	+: 7/22 −: 23/23	0.32	1.00	1.00	0.61	0.67
ApoA4 and ApoE	+: 20/22 −: 22/23	0.91	0.96	0.95	0.92	0.93
ApoA4, ApoE, Clusterin	+: 22/22 −: 23/23	1.00	1.00	1.00	1.00	1.00
ApoA4, ApoE, Vitronectin	+: 22/22 −: 22/23	1.00	0.96	0.96	1.00	0.98
ApoA4, ApoE, Complement C9	+: 22/22 −: 22/23	1.00	0.96	0.96	1.00	0.98
ApoA4, ApoE, Collagen alpha−1(VI) chain	+: 20/22 −: 22/23	0.91	0.96	0.95	0.92	0.93
ApoA4, ApoE, Collagen alpha−2(VI) chain	+: 20/22 −: 23/23	0.91	1.00	1.00	0.92	0.96
ApoA4, ApoE, Collagen alpha−3(VI) chain	+: 21/22 −: 22/23	0.95	0.96	0.95	0.96	0.96
ApoA4, ApoE, Fibulin−1	+: 20/22 −: 23/23	0.91	1.00	1.00	0.92	0.96
ApoA4, ApoE and SAP	+: 22/22 −: 23/23	1.00	1.00	1.00	1.00	1.00