Table 3.
Performance comparison of MZmine 2 alignment methods (right side of the table) to previously published results (left side of the table) obtained using several different software packages [11].
| Results published by Lange et al. (2008), avaiable at the time of writing at http://msbi.ipb-halle.de/msbi/caap | MZmine 2 results | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| msInspect | MZmine (version 0.6) |
OpenMS | SpecArray | XAlign | XCMS | ||||
| without RT correction | With correction | Join aligner | RANSAC aligner | ||||||
| Proteomics data set P1 | |||||||||
| fraction 00 | |||||||||
| Recall | 0.52 | 0.81 | 0.86 | 0.61 | 0.82 | 0.72 | 0.62 | 0.80 | 0.86 |
| Precision | 0.38 | 0.81 | 0.86 | 0.61 | 0.82 | 0.54 | 0.58 | 0.80 | 0.86 |
| fraction 20 | |||||||||
| Recall | 0.56 | 0.90 | 0.92 | 0.62 | 0.85 | 0.88 | 0.81 | 0.90 | 0.93 |
| Precision | 0.45 | 0.90 | 0.92 | 0.62 | 0.85 | 0.84 | 0.80 | 0.90 | 0.93 |
| fraction 40 | |||||||||
| Recall | 0.63 | 0.90 | 0.94 | 0.75 | 0.87 | 0.92 | 0.81 | 0.87 | 0.94 |
| Precision | 0.48 | 0.90 | 0.94 | 0.75 | 0.87 | 0.85 | 0.80 | 0.87 | 0.94 |
| fraction 60 | |||||||||
| Recall | 0.73 | 0.84 | 0.96 | 0.71 | 0.87 | 0.91 | 0.78 | 0.89 | 0.97 |
| Precision | 0.54 | 0.84 | 0.96 | 0.71 | 0.87 | 0.80 | 0.75 | 0.89 | 0.97 |
| fraction 80 | |||||||||
| Recall | 0.70 | 0.94 | 0.96 | 0.74 | 0.90 | 0.94 | 0.89 | 0.94 | 0.97 |
| Precision | 0.57 | 0.94 | 0.96 | 0.74 | 0.90 | 0.88 | 0.88 | 0.94 | 0.97 |
| fraction 100 | |||||||||
| Recall | 0.82 | 0.94 | 0.94 | 0.77 | 0.96 | 0.95 | 0.96 | 0.95 | 0.96 |
| Precision | 0.56 | 0.94 | 0.94 | 0.77 | 0.96 | 0.89 | 0.96 | 0.95 | 0.96 |
| Proteomics data set P2 | |||||||||
| fraction 00 | |||||||||
| Recall | 0.23 | 0.62 | 0.77 | 0.07 | 0.65 | 0.70 | 0.58 | 0.63 | 0.56 |
| Precision | 0.07 | 0.49 | 0.65 | 0.05 | 0.49 | 0.31 | 0.44 | 0.53 | 0.49 |
| fraction 20 | |||||||||
| Recall | 0.67 | 0.87 | 0.92 | 0.57 | 0.84 | 0.89 | 0.86 | 0.81 | 0.93 |
| Precision | 0.24 | 0.71 | 0.77 | 0.42 | 0.70 | 0.55 | 0.66 | 0.69 | 0.78 |
| fraction 40 | |||||||||
| Recall | 0.44 | 0.79 | 0.76 | 0.60 | 0.71 | 0.72 | 0.72 | 0.74 | 0.78 |
| Precision | 0.26 | 0.76 | 0.74 | 0.41 | 0.69 | 0.56 | 0.69 | 0.73 | 0.77 |
| fraction 80 | |||||||||
| Recall | 0.73 | 0.60 | 0.80 | 0.65 | 0.58 | 0.64 | 0.49 | 0.61 | 0.61 |
| Precision | 0.34 | 0.56 | 0.70 | 0.44 | 0.56 | 0.50 | 0.45 | 0.58 | 0.61 |
| fraction 100 | |||||||||
| Recall | 0.82 | 0.80 | 0.90 | 0.63 | 0.85 | 0.95 | 0.85 | 0.85 | 0.88 |
| Precision | 0.39 | 0.64 | 0.75 | 0.44 | 0.69 | 0.65 | 0.69 | 0.71 | 0.75 |
| Metabolomics data sets | |||||||||
| M1 | |||||||||
| Recall | 0.27 | 0.92 | 0.87 | - | 0.88 | 0.98 | 0.94 | 0.90 | 0.91 |
| Precision | 0.46 | 0.73 | 0.69 | - | 0.70 | 0.60 | 0.70 | 0.74 | 0.74 |
| M2 | |||||||||
| Recall | 0.23 | 0.98 | 0.93 | - | 0.93 | 0.97 | 0.98 | 0.98 | 0.98 |
| Precision | 0.47 | 0.84 | 0.79 | - | 0.79 | 0.58 | 0.78 | 0.83 | 0.83 |