Table 1

Influence of background removal on the recovery of BSA, ADH and TRF in MS/MS spectra of 100 fmol test samples. The original number of MS/MS spectra for the BSA (bovine serum albumine), ADH (yeast alcoholdehydrogenase) and TRF (human transferring) datasets (recorded on a DecaXP machine) are 2679, 2325 and 2608 respectively. The intensity threshold s (column 3) describes the search of the sequence ladder (length n in column 2) within the 15%, 20%, 25% or 30% top peaks (100% - all peaks are considered). The following three columns show the MS Cleaner output - number of spectra with background removal, number of unselected spectra and the MS Cleaner CPU time on a single-processor Windows XP computer (Pentium IV 2.4 GHz; to get exact measurements of computation time, we did not use the cluster version). The remaining four columns present the MASCOT output - the CPU time on the same machine, the protein score, the number of spectra matching peptides in a MASCOT search and the final sequence coverage. For each dataset, the first line shows the results for the case when MS Cleaner is not used for pre-processing and the MS/MS data is immediately interpreted by MASCOT.

protein

sequence ladder length n

intensity threshold s [%]

cleaned spectra

bad spectra

MS Cleaner time [min]

MASCOT time [min]

MASCOT score

queries matched

sequence coverage


BSA

0

100

-

-

-

61

586

89

55


3

100

1664

1015

3.92

44

720

91

57

3

15

390

2289

1.21

17

1991

84

52

3

20

490

2189

1.40

21

2108

87

57

3

25

601

2078

1.61

26

2114

89

57

3

30

688

1991

1.75

29

2114

90

57


4

100

940

1739

3.80

36

2108

91

57

4

15

260

2419

0.91

12

1875

78

47

4

20

321

2358

1.06

14

1911

80

47

4

25

380

2299

1.25

18

2114

86

57

4

30

441

2238

1.30

19

2114

89

57


5

100

593

2086

3.82

26

2108

91

57

5

15

174

2505

0.60

9

1579

60

41

5

20

232

2447

0.85

11

1809

72

44

5

25

281

2398

1.00

13

1963

81

49

5

30

313

2366

0.85

14

2058

86

54


ADH

0

100

-

-

-

64

242

39

39


3

100

1446

879

4.15

45

327

34

39

3

15

269

2056

0.88

12

673

29

35

3

20

347

1978

1.10

13

696

31

37

3

25

440

1885

1.33

17

697

32

37

3

30

697

1628

1.53

20

697

33

37


4

100

902

1423

4.15

35

733

34

39

4

15

173

2152

0.58

7

562

26

28

4

20

216

2109

0.71

9

673

30

35

4

25

271

2054

0.90

12

607

28

33

4

30

325

2000

1.05

13

697

32

37


5

100

594

1731

4.20

23

712

33

39

5

15

94

2231

0.35

5

311

15

21

5

20

125

2200

0.46

6

366

17

25

5

25

145

2180

0.53

7

434

19

26

5

30

186

2139

0.66

9

589

24

31


TRF

0

100

-

-

-

52

588

86

47


3

100

1587

1021

3.57

42

768

87

49

3

15

373

2235

1.00

17

1988

86

49

3

20

485

2123

1.23

20

1988

86

49

3

25

568

2040

1.36

24

1998

87

49

3

30

639

1969

0.78

27

1998

87

49


4

100

864

1744

3.62

34

1973

87

49

4

15

231

2377

0.70

11

1987

81

49

4

20

298

2310

0.86

13

1988

84

49

4

25

360

2248

1.00

16

1988

85

49

4

30

414

2194

1.12

19

1998

87

49


5

100

540

2068

3.63

23

1973

87

49

5

15

164

2444

0.55

9

1785

68

45

5

20

194

2414

0.61

10

1890

74

47

5

25

245

2363

0.75

12

1957

80

48

5

30

286

2322

0.86

14

1968

84

48


Mujezinovic et al. BMC Genomics 2010 11(Suppl 1):S13   doi:10.1186/1471-2164-11-S1-S13

Open Data