Skip to main content

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].

From: MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

  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