Table 2 The normalized computing times of the three search engines on eight datasets

From: A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

Dataset

pLink 1

Kojak

pLink 2

Real timea

Simulated-BS3

24.6

3.4

1.0

0.5

Simulated-SS

12.7

1.7

1.0

0.7

Synthetic-BS3 + Original

35.5

2.3

1.0

0.1

Synthetic-BS3 + E. coli

45.4

1.7

1.0

0.5

Synthetic-BS3 + Worm

50.8

2.4

1.0

3.5

Synthetic-BS3 + Human

38.3

2.1

1.0

6.4

Synthetic-SS + Original

32.7

2.6

1.0

0.2

Synthetic-SS + E. coli

60.2

3.3

1.0

1.2

Synthetic-SS + Worm

64.3

3.8

1.0

17.7

Synthetic-SS + Human

69.7

4.0

1.0

31.9

E.coli-Leiker-15N

31.4

1.6

1.0

142.9

E.coli-SS-15N

62.6

4.2

1.0

200.7

SCF(FBXL3)-BS3 + Original

20.0

1.7

1.0

260.6

SCF(FBXL3)-BS3 + E. coli

46.0

3.8

1.0

22.0

SCF(FBXL3)-BS3 + Worm

b

4.5

1.0

275.7

SCF(FBXL3)-BS3 + Human

b

4.2

1.0

385.1

Cav1.1-SS + Original

20.4

2.7

1.0

2.9

Cav1.1-SS + E. coli

31.8

3.4

1.0

1.8

Cav1.1-SS + Worm

36.1

4.0

1.0

34.5

Cav1.1-SS + Human

40.2

5.1

1.0

45.7

Average

40.2

3.1

1.0

  1. aThe real search times for pLink 2 are shown in minutes
  2. bpLink 1 did not finish searching against the worm or the human entrapment databases within 1 week when five variable modifications were set