Table 3. PPVs and NPVs for Different Combinations of Parameters and Methods (Imputation and Normalization) on the Peptide Levela.
| Source | Tool (imputation-normalization) | UPS spiked data set |
Tool (imputation-normalization) | Large-scale data set (4:1 fold) |
Tool (imputation-normalization) | Large-scale data set (10:1 fold) |
|||
|---|---|---|---|---|---|---|---|---|---|
| PPV | NPV | PPV | NPV | PPV | NPV | ||||
| quantms | MSstats (NaN-Q) | 0.91 (30 TP, total 1896) | 0.995 (10 FN) | MSstats (NaN-NN) | 0.86 (554 TP, total 2740) | 0.934 (137 FN) | MSstats (NaN-NN) | 0.73 (628 TP, total 2740) | 0.966 (63 FN) |
| Proteus (MVL-EM) | 0.91 (33 TP, total 1905) | 0.997 (6 FN) | Proteus (MVL-NN) | 0.75 (386 TP, total 2587) | 0.928 (147 FN) | Proteus (MVL-NN) | 0.66 (450 TP, total 2587) | 0.952 (88 FN) | |
| msqrob2 (NaN-CM) | 0.80 (12 TP, total 1657) | 0.990 (16 FN) | msqrob2 (NaN-NN) | 0.87 (388 TP, total 2310) | 0.953 (88 FN) | msqrob2 (NaN-NN) | 0.82 (423 TP, total 2310) | 0.970 (53 FN) | |
| MaxQuant | MSstats (NaN-Q) | 0.90 (36 TP, total 2116) | 0.999 (1 FN) | MSstats (NaN-NN) | 0.90 (589 TP, total 2576) | 0.973 (47 FN) | MSstats (NaN-NN) | 0.85 (619 TP, total 2478) | 0.990 (18 FN) |
| Proteus (MVL-EM) | 0.89 (34 TP, total 2115) | 1.0 (0 FN) | Proteus (MVL-NN) | 0.64 (308 TP, total 2418) | 0.964 (70 FN) | Proteus (MVL-NN) | 0.55 (343 TP, total 2314) | 0.976 (40 FN) | |
| msqrob2 (NaN-CM) | 0.87 (33 TP, total 2116) | 0.999 (1 FN) | msqrob2 (NaN-Q) | 0.81 (325 TP, total 2232) | 0.982 (33 FN) | msqrob2 (NaN-Q) | 0.53 (348 TP, total 2232) | 0.994 (10 FN) | |
a
*: No shared peptides, >2 unique peptides per protein. Only the best combination for each tool is presented. Supplementary Table 5 contains all combinations’ results.