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Table 6 Comparison between searches against databases of different sizes

From: False discovery rates in spectral identification

Search#

Spectra

Database

PMTol

DB size

EmpiricalFDR fixed

FactFDR fixed

     

N target

FactFDR(%)

p-value(%)

N target

EmpiricalFDR(%)

I-1

ISB-02

ISB

2.5 Da

7,440

2329/1009

5.8/4.4

10.9/30.9

2279/1024

3.9/5.7

I-3

ISB-02

ISB+Yeast

2.5 Da

3,019,432

1578/602

4.7/5.1

40.8/50.3

1583/596

5.1/3.9

I-14

ISB-02+AB-TC

ISB

2.5 Da

7,440

2262/984

5.8/4.5

5.7/34.5

2221/995

4.0/6.0

I-5

ISB-02+AB-TC

ISB+Yeast

2.5 Da

3,019,432

1490/569

5.0/5.8

50.2/31.2

1480/553

4.5/4.3

I-7

ISB-02+AB-TC

ISB+AT

2.5 Da

13,475,763

1320/441

4.6/4.1

36.6/38.0

1342/464

5.8/7.3

Y-5

Y-Small+AB-TC

Yeast

30 ppm

3,011,992

3340/2734

1.2/1.0

30.0/50.1

3209/2717

0.8/1.0

Y-1

Y-Small+AB-TC

Yeast+AT

30 ppm

16,480,315

2574/1988

1.0/1.3

50.1/22.7

2588/1759

1.0/0.5

  1. As expected, for smaller databases, TDA yielded more resulting PSMs. Fisher p-values were higher than 5% for all cases, which indicates that the FDR estimation via empirical FDR is reliable regardless of the database size.