Table 6

For MsPI 1, Mascot 1 and Piums the mass tolerance was set to 0.3 Da; in the other cases it was set to 100 ppm. For MsPI 1, MsPI 2 and MsPI 3, score 1, 2 and 3 were respectively used with uniform distribution. For each band the position of the "true" protein in the significant candidate list, the length of that list either using or not using the knowledge about the MW of the band, the MW and the pI of the "true" protein, the number of matching masses and the sequence coverage are reported.

Gel band (#)

Software tool

Rank (# significant proteins without MW filtering)

Rank (# significant proteins with MW filtering)

MW (Da)

pI

Matches (#)

Coverage (%)

1

MsPI 1

2 (2)

1 (1)

123852

5.31

23

0.267

MsPI 2

7 (8)

1 (1)

123852

5.31

23

0.270

MsPI 3

2 (2)

1 (1)

123852

5.31

23

0.267

Mascot 1

1 (1)

1 (1)

124292

5.50

23

0.250

Mascot 2

1 (1)

1 (1)

124292

5.50

23

0.250

Piums

-

- (-)

-

-

21

0.242

2

MsPI 1

1 (2)

1 (1)

191785

5.32

36

0.252

MsPI 2

1 (4)

1 (1)

191785

5.32

35

0.252

MsPI 3

1 (2)

1 (1)

191785

5.32

35

0.252

Mascot 1

1 (1)

1 (1)

193260

5.48

36

0.250

Mascot 2

1 (3)

1 (1)

193260

5.48

35

0.250

Piums

1 (1)

-

-

-

36

0.257

3

MsPI 1

2 (8)

1 (1)

104981

5.08

21

0.245

MsPI 2

- (4)

- (-)

104981

5.08

21

0.245

MsPI 3

2 (4)

1 (1)

104981

5.08

21

0.245

Mascot 1

1 (2)

1 (1)

105245

5.27

21

0.240

Mascot 2

1 (6)

1 (2)

105245

5.27

21

0.240

Piums

- (-)

-

-

-

19

0.254

4

MsPI 1

2 (4)

1 (1)

95382

6.38

20

0.286

MsPI 2

1 (5)

1 (1)

95382

6.38

20

0.286

MsPI 3

1 (6)

1 (2)

95382

6.38

20

0.286

Mascot 1

1 (1)

1 (1)

96246

6.41

22

0.320

Mascot 2

1 (1)

1 (1)

96246

6.41

22

0.320

Piums

- (-)

-

-

-

19

0.341

5

MsPI 1

2 (8)

2 (3)

84351

4.70

28

0.418

MsPI 2

3 (3)

2 (2)

84351

4.70

28

0.418

MsPI 3

2 (12)

2 (3)

84351

4.70

28

0.418

Mascot 1

1 (2)

1 (2)

83554

4.97

35

0.480

Mascot 2

1 (3)

1 (2)

83554

4.97

34

0.480

Piums

1 (1)

-

-

-

28

0.364

6

MsPI 1

2 (8)

1 (1)

67900

7.37

24

0.515

MsPI 2

- (1)

- (-)

67900

7.37

23

0.509

MsPI 3

1 (6)

1 (1)

67900

7.37

23

0.509

Mascot 1

1 (2)

1 (1)

68519

7.58

24

0.510

Mascot 2

1 (4)

1 (2)

68519

7.58

23

0.500

Piums

- (-)

-

-

-

19

0.446

7

MsPI 1

1 (3)

1 (1)

53146

4.82

21

0.468

MsPI 2

1 (2)

1 (1)

53146

4.82

21

0.468

MsPI 3

1 (2)

1 (1)

53146

4.82

21

0.468

Mascot 1

1 (1)

1 (1)

53676

5.06

21

0.500

Mascot 2

1 (3)

1 (1)

53676

5.06

21

0.500

Piums

- (-)

-

-

-

16

0.413

8

MsPI 1

- (2)

- (-)

49674

4.53

8

0.232

MsPI 2

- (1)

- (-)

49674

4.53

8

0.232

MsPI 3

- (1)

- (-)

49674

4.53

8

0.232

Mascot 1

- (-)

- (-)

50095

4.78

8

0.230

Mascot 2

- (-)

- (-)

50095

4.78

8

0.230

Piums

- (-)

-

-

-

8

0.232

9

MsPI 1

1 (4)

1 (1)

45982

9.79

31

0.784

MsPI 2

1 (4)

1 (1)

45982

9.79

32

0.787

MsPI 3

1 (5)

1 (1)

45982

9.79

32

0.787

Mascot 1

1 (1)

1 (1)

46180

9.45

31

0.730

Mascot 2

1 (1)

1 (1)

46180

9.45

31

0.730

Piums

1 (1)

-

-

-

27

0.715

10

MsPI 1

1 (9)

1 (2)

41611

5.10

13

0.349

MsPI 2

2 (5)

2 (2)

41611

5.10

13

0.379

MsPI 3

1 (6)

1 (4)

41611

5.10

13

0.379

Mascot 1

1 (4)

1 (4)

42052

5.29

13

0.370

Mascot 2

1 (4)

1 (4)

42052

5.29

13

0.370

Piums

2 (2)

-

-

-

13

0.380

Tiengo et al. BMC Bioinformatics 2009 10(Suppl 12):S11   doi:10.1186/1471-2105-10-S12-S11

Open Data