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Table 4 Evaluation of filter performance. This table presents the classification rates of the identified spectra for varying fractions of the significance threshold with and without retention time filtering. The model was trained using the vds3 dataset and the performance was measured on ds1 and ds2. In this context, tp stands for the number of true positives and fp for the number of false positives. The CR is tp divided by the sum of tp and fp.

From: Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics

Fraction of threshold

tp

fp

CR

tp with filter

fp with filter

CR with filter

0.0

683

2572

0.2098

699

626

0.5275

0.1

682

2460

0.2171

692

602

0.5348

0.2

678

2260

0.2308

683

555

0.5517

0.3

669

1909

0.2595

668

483

0.5804

0.4

654

1410

0.3169

646

380

0.6296

0.5

624

868

0.4182

609

261

0.7000

0.6

575

474

0.5481

557

166

0.7704

0.7

516

235

0.6871

500

103

0.8292

0.8

468

125

0.7892

452

66

0.8726

0.9

420

72

0.8537

404

49

0.8918

1.0

366

46

0.8883

350

38

0.9021