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Critical Assessment of Alignment Procedures

Data and evaluation scripts

 

Eva Lange, Ralf Tautenhahn, Steffen Neumann and Clemens Gröpl

"Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements"

BMC Bioinformatics 2008, 9:375

Errata

Supplementary table 3: M1 and M2 labels are inverted in the table.

 

Proteomics data

The P1 and P2 raw data sets were previously available at the "Open Proteomics Database", which seems to be out of service. We have provided a copy of the raw data here, see below.

 

P1 feature data (featureXML) and P1 raw data (mzXML)

P1 ground truth data (space-separated)

 

P2 feature data (featureXML) and P2 raw data (mzXML)

 

 

P2 ground truth data (space-separated)

 

Notes on the P1,P2 ground truth file format

 

Metabolomics data

M1 feature data (featureXML) M1 raw data (mzData)

 

M1 ground truth data (space-separated)

 

M2 feature data (featureXML) M2 raw data (netCDF)

 

M2 ground truth data (space-separated)

 

Notes on the M1,M2 ground truth file format

 

Evaluation script

CAAP Evaluation (R-)Script V1.1

 

Notes on the Evaluation Script

 

 

Results using eval.R v1.1

 

Alignment recall and precision results for the proteomics data set P1

 


msInspect mzMine OpenMS SpecArray XAlign XCMS /wo RC XCMS /w RC
fraction 00






recall 0.5 0.81 0.86 0.61 0.82 0.72 0.62
precision 0.37 0.81 0.86 0.61 0.82 0.54 0.59








fraction 20






recall 0.55 0.9 0.93 0.61 0.85 0.89 0.88
precision 0.47 0.9 0.93 0.61 0.85 0.84 0.88








fraction 40






recall 0.52 0.9 0.93 0.74 0.87 0.92 0.81
precision 0.41 0.9 0.93 0.74 0.87 0.85 0.79








fraction 60






recall 0.58 0.84 0.96 0.71 0.87 0.91 0.77
precision 0.48 0.84 0.96 0.71 0.87 0.8 0.75








fraction 80






recall 0.62 0.94 0.97 0.74 0.9 0.94 0.9
precision 0.55 0.94 0.97 0.74 0.9 0.88 0.89








fraction 100






recall 0.81 0.94 0.96 0.77 0.96 0.95 0.96
precision 0.58 0.94 0.96 0.77 0.96 0.89 0.96

 


Alignment recall and precision results for the proteomics data set P2

 


msInspect mzMine OpenMS SpecArray XAlign XCMS /wo RC XCMS /w RC
fraction 00






recall 0.01 0.62 0.77 0.07 0.64 0.55 0.45
precision 0.01 0.49 0.65 0.05 0.51 0.32 0.39








fraction 20






recall 0.47 0.87 0.92 0.57 0.68 0.88 0.87
precision 0.37 0.71 0.76 0.42 0.60 0.61 0.71








fraction 40






recall 0.36 0.79 0.76 0.60 0.72 0.74 0.56
precision 0.27 0.76 0.74 0.41 0.70 0.69 0.55








fraction 80






recall 0.61 0.60 0.80 0.66 0.57 0.49 0.44
precision 0.38 0.56 0.70 0.45 0.56 0.42 0.43








fraction 100






recall 0.64 0.80 0.90 0.63 0.83 0.80 0.76
precision 0.43 0.64 0.75 0.44 0.69 0.62 0.64

 

Alignment recall and precision results for the metabolomics data sets M1 and M2

 


msInspect mzMine OpenMS SpecArray XAlign XCMS /wo RC XCMS /w RC
M1






Recall 0.12 0.92 0.87 - 0.88 0.97 0.94
Precision 0.68 0.73 0.69 - 0.7 0.59 0.7
















M2






Recall 0.12 0.98 0.93 - 0.92 0.97 0.98
Precision 0.49 0.84 0.79 - 0.78 0.58 0.78

 

Comments, questions and new results

rtautenh (at) scripps (dot) edu

sneumann (at) ipb-halle (dot) de