Table 2 Summary of the running times for various search parameter settings

A (unit: second)

 1. Comet search

7846.9

7967.0

8320.1

15,084.1

25,650.1

34,287.5

 2-a. Comet-P (without E-value)

459.1

447.9

442.0

528.0

575.3

635.9

 2-b. Comet-E (with E-value)

1900.1

1709.3

1711.2

1911.1

2035.3

2075.7

  2.1. Database separation

3.7

3.3

3.1

3.3

3.0

3.0

  2.2. Deletion

244.1

228.2

223.1

261.5

280.2

344.3

   2.2.1. Extract spectra

14.8

15.9

14.4

16.6

14.2

15.6

   2.2.2. Comet-P/E search

72.5

57.9

58.4

78.5

91.8

158.7

   2.2.3. Update results

156.9

154.3

150.3

166.4

174.2

170.0

  2.3. Insertion

211.3

216.4

215.7

263.1

292.1

288.6

   2.3.1. Comet-P/E search

168.9

168.6

162.9

192.6

216.1

213.7

   2.3.2. Update results

42.4

47.8

52.8

70.5

76.0

74.9

  2.4. E-value calculation

1441.0

1261.4

1269.3

1383.1

1459.9

1439.8

B

 The running time ratio

  Comet-P

5.85%

(× 17.09)

5.62%

(× 17.79)

5.31%

(× 18.82)

3.50%

(× 28.57)

2.24%

(× 44.59)

1.85%

(× 53.92)

  Comet-E

24.21%

(× 4.13)

21.45%

(× 4.66)

20.57%

(× 4.86)

12.67%

(× 7.89)

7.93%

(× 12.60)

6.05%

(× 16.52)

  Deletion

3.11%

2.86%

2.68%

1.73%

1.09%

1.00%

  Insertion

2.69%

2.72%

2.59%

1.74%

1.14%

0.84%

  E-value

calculation

18.36%

15.83%

15.26%

9.17%

5.69%

4.20%

 Database size ratio

  |D_del |/|D_new|*

0.02% (8821 / 56,400,212)

  |D_ins|/|D_new|*

0.14% (76,988 / 56,400,212)

Deleted PSMs ratio (|S_del|/|S|)

0.02%

(221 / 1,121,149)

0.02%

(249 / 1,121,149)

0.02%

(261 / 1,121,149)

0.02%

(222 / 1,121,149)

0.02%

(221 / 1,121,149)

0.02%

(226 / 1,121,149)