Table 2 Evaluation measures for 2023 commonly quantifiable proteins of the four software tools on Hultin-iTRAQ8.

From: Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage

 

MTQ_alg1

MTQ_alg2

MaxQuant

Libra

PatternLab

AUCCD

0.901

0.905*

0.889

0.894

0.899

ARE

0.090

0.086

0.102

0.094

0.091

RMSE

0.220

0.218

0.243

0.228

0.226

Mean1#

0.955

0.964

1.102

0.989

0.966

Mean2

1.964

1.981

2.099

1.993

1.970

SD1

0.155

0.148

0.148

0.156

0.136

SD2

0.253

0.256

0.263

0.269

0.271

  1. *Boldface indicates the best measure among the tools.
  2. #Since this standard data set has an ideal protein ratio of either 1 or 2, we use Mean1 and SD1 to represent mean and standard deviation of protein ratios with an ideal value of 1, and use Mean2 and SD2 to represent mean and standard deviation of protein ratios with an ideal value of 2.
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