Table 5 Comparison of different methods on the complex datasets

Confirmed matches

Non-redundant peptides

Proteins*

Proteins with at least 2/3 peptide hits (%)

Confirmed matches

Non-redundant peptides

Proteins*

Proteins with at least 2/3 peptide hits (%)

LCQ

M1

13,636

5,268

1,922

51.1/35.2

11,512

4,496

1,630

54.0/36.0

M2

14,128

5,333

1,860

53.7/36.4

10,436

4,219

1,586

53.3/34.4

M3

15,923

5,872

2,077

52.6/36.2

13,549

5,084

1,729

55.9/38.3

LTQ

M1

45,153

10,359

3,363

54.6/37.6

36,857

8,601

2,733

58.3/39.3

M2

40,791

10,053

3,166

55.2/39.1

30,696

7,875

2,488

58.7/40.3

M3

52,569

11,451

3,421

57.9/40.9

44,576

9,756

2,801

61.6/43.1

LTQ/FT

M1

25,672

4,602

2,723

42.0/23.0

22,750

3,869

2,193

42.5/22.8

M2

23,571

3,947

2,462

45.2/25.4

19,930

3,366

2,083

45.4/24.9

M3

27,565

4,855

2,820

43.7/24.8

25,185

4,196

2,291

45.6/25.7