Table 3 Summary of the running times for several database update intervals

A (unit: second)

 1. Comet search

34,287.5

35,073.6

35,052.1

34,840.2

35,559.4

 2-a. Comet-P (without E-value)

635.9

1282.6

1439.5

1532.8

2045.3

 2-b. Comet-E (with E-value)

2075.7

2779.3

2834.0

2960.5

3476.1

  2.1. Database separation

3.0

3.0

3.0

3.2

3.1

  2.2. Deletion

344.3

410.0

459.0

498.8

598.3

   2.2.1. Extract spectra

15.6

15.8

15.0

16.3

15.7

   2.2.2. Comet-P/E search

158.7

184.9

199.5

216.2

251.7

   2.2.3. Update results

170.0

209.3

244.5

266.3

330.8

  2.3. Insertion

288.6

869.6

977.5

1030.8

1443.9

   2.3.1. Comet-P/E search

213.7

787.8

893.9

946.9

1354.8

   2.3.2. Update results

74.9

81.8

83.6

83.9

89.1

  2.4. E-value calculation

1439.8

1496.7

1394.5

1427.8

1430.8

B

The running time ratio

 Comet-P

1.85%

(× 53.92)

3.66%

(× 27.35)

4.11%

(× 24.35)

4.40%

(× 22.73)

5.75%

(× 17.39)

 Comet-E

6.05%

(× 16.52)

7.92%

(× 12.62)

8.09%

(× 12.37)

8.50%

(× 11.77)

9.78%

(× 10.23)

 Deletion

1.00%

1.17%

1.31%

1.43%

1.68%

 Insertion

0.84%

2.48%

2.79%

2.96%

4.06%

 E-value

calculation

4.20%

4.27%

3.98%

4.10%

4.02%

Database size ratio

 |D_del |/|D_new|*

0.02%

(8821 / 56,400,212)

0.11%

(64,323 / 57,348,066)

0.21%

(118,748 / 57,471,311)

0.26%

(149,505 / 57,516,232)

0.44%

(252,754 / 58,101,266)

 |D_ins|/|D_new|*

0.14%

(76,988 / 56,400,212)

1.88%

(1,080,344 / 57,348,066)

2.19%

(1,258,014 / 57,471,311)

2.32%

(1,333,692 / 57,516,232)

3.48%

(2,021,975 / 58,101,266)

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

0.02%

(226 / 1,121,149)

0.10%

(1121 / 1,121,149)

0.15%

(1717 / 1,121,149)

0.21%

(2410 / 1,121,149)

0.31%

(3426 / 1,121,149)