Table 2

Overlap of identified peptides and proteins between algorithms with a FDR < 2%

Algorithm

Peptides

RefSeq

Proteins

Putative

Isoforms




Count

%

Count

%

Count

%


Mascot only

275

7.1

58

5.2

6

8.3

OMSSA only

152

3.9

72

6.5

8

11.1

X! Tandem only

471

12.1

156

14.0

23

31.9

InsPecT only

334

8.6

98

8.8

20

27.8

Mascot, OMSSA

115

3.0

24

2.2

0

0.0

Mascot, X! Tandem

100

2.6

13

1.2

2

2.8

Mascot, InsPecT

80

2.1

10

0.9

1

1.4

OMSSA, X! Tandem

30

0.8

17

1.5

0

0.0

OMSSA, InsPecT

44

1.1

5

0.4

0

0.0

X! Tandem, InsPecT

108

2.8

12

1.1

0

0.0

Mascot, OMSSA, X! Tandem

185

4.8

36

3.2

0

0.0

Mascot, OMSSA, InsPecT

209

5.4

16

1.4

1

1.4

Mascot, X! Tandem, InsPecT

116

3.0

22

2.0

0

0.0

OMSSA, X! Tandem, InsPecT

21

0.5

7

0.6

0

0.0

Mascot, OMSSA, X! Tandem, InsPecT

1651

42.4

568

51.0

11

15.3

Grand Total

3891

100.0

1114

100.0

72

100.0


Chang and Muddiman BMC Genomics 2011 12:358   doi:10.1186/1471-2164-12-358

Open Data