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Table 4 Comparison between concatenated-decoy searches and separate-decoy searches

From: False discovery rates in spectral identification

Search#

Spectra

Database

PMTol

Decoy

EmpiricalFDR fixed

FactFDR fixed

     

N target

FactFDR(%)

p-value(%)

N target

EmpiricalFDR(%)

I-1

ISB-02

ISB

2.5 Da

Rev

2329/1009

5.8/4.4

10.9/30.9

2279/1024

3.9/5.7

I-9

ISB-02

ISB

2.5 Da

Sep.Rev

2159/941

2.1/2.4

0.0/0.4

2287/1028

8.6/12.2

I-5

ISB-02+AB-TC

ISB+Yeast

2.5 Da

Rev

1490/569

5.0/5.8

50.2/31.2

1480/553

4.5/4.3

I-10

ISB-02+AB-TC

ISB+Yeast

2.5 Da

Sep.Rev

1462/504

4.6/3.6

40.3/18.7

1482/544

5.3/7.9

I-7

ISB-02+AB-TC

ISB+AT

2.5 Da

Rev

1320/441

4.6/4.1

36.6/38.0

1342/464

5.8/7.3

I-11

ISB-02+AB-TC

ISB+AT

2.5 Da

Sep.Rev

1287/453

3.4/4.9

3.7/56.1

1342/456

7.0/5.5

Y-1

Y-Small+AB-TC

Yeast+AT

30 ppm

Rev

2574/1988

1.0/1.3

50.1/22.7

2588/1759

1.0/0.5

Y-3

Y-Small+AB-TC

Yeast+AT

30 ppm

Sep.Rev

2501/1605

0.8/.0.7

33.1/28.7

2589/1759

1.4/1.5

  1. All searches followed the standard TDA procedure except the step 2 for separate reverse database searches. The search I-9 demonstrates that the separate-decoy searches result in more conservative FDR estimation than concatenated-decoy searches, in particular for small databases.