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Table 4 Validation of AuDIT.

From: Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics

Dataset Annotation TN TP FN FP Overall Accuracy (%) Sensitivity (%) Specificity (%)
10 Peptide Standard Curve, 3 transitions MultiQuant Site 1 Global 89
11
119 29 33 77 80 73
   Focused 7 144 1 8 97 99 94
  Site 2 Global 9 217 14 30 84 94 23
   Focused 23 247 0 0 100 100 100
  Site 3 Global 19 200 33 18 81 86 51
   Focused 50 218 2 0 99 99 100
  Site 4 Global 21 162 74 13 68 69 62
   Focused 81 174 14 1 94 93 99
10 Peptide Standard Curve, 3 transitions, Skyline Site 1 Global 29 163 35 43 71 82 40
   Focused 56 206 8 0 97 96 100
  Site 2 Global 1 210 15 44 78 93 2
   Focused 15 254 1 0 100 100 100
  Site 5 Global 35 34 2 199 26 94 15
   Focused 37 232 0 1 100 100 97
10 Peptide Standard Curve, 5 transitions, MultiQuant Site 6 Global 46
16
277 122 23 69 69 67
   Focused 8 294 0 6 99 100 97
Clinical Samples, 3 transitions, MultiQuant Cardio-vascular Peptides Global 4 33 5 9 73 87 31
   Focused 9 40 0 2 96 100 82
  1. For each dataset, two contingency matrices are calculated. The 'pre-test' evaluation by the expert identifies overall data problems like poor chromatography, inaccurate peak integration, etc. Comparison of this global annotation with the algorithm calls results in one set of contingency matrices (shown under Annotation = Global). The second 'post-test' re-evaluation is based on the algorithm outcome, and accounts for the fact that the global annotation could be overly conservative (i.e., mark too many transitions as BAD). This focused annotation is compared with the algorithm-derived decisions to derive a second, algorithm-guided set of contingency matrices, shown under Annotation = Focused. TN: True Negative, TP: True Positive, FN: False Negative, and FP: False Positive. Overall Accuracy = (TP + TN)/(TP + TN + FN + FP). Sensitivity = TP/(TP + FN). Specificity = TN/(TN + FP). A transition is BAD if it has some form of interference, i.e., it is imprecise of inaccurate. If not, the transition is labeled as GOOD. Adapted from Abbatiello, Mani, et. al., Clinical Chemistry, 56, 291-305 [17].
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