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Table 1 Summary data showing stages in the quality assessment of QC sample spectra.

From: A method for improving SELDI-TOF mass spectrometry data quality

Analysis Step

QC Data Set

Pearson Correlation Coefficient (Grand Mean ± Std Dev)

No. spectra

No peaks

Coefficient of Variation (%)

     

Low

High

Average

% Peaks CV < 30%

A

CMHS_F3

0.834 ± 0.225

66

58

15.1

199.2

44.8

34

 

CMHS_F4

0.829 ± 0.135

66

37

14.1

84.7

37.9

27

 

CMLS_F1

0.946 ± 0.038

66

68

8.0

48.1

22.5

82

 

CMLS_F3

0.851 ± 0.142

66

72

7.8

50.1

26.3

69

 

CMLS_F4

0.918 ± 0.110

66

54

9.8

53.7

24.1

76

 

CMLS_F5

0.879 ± 0.146

66

54

10.5

274.4

32.9

70

 

CMLS_F6

0.904 ± 0.173

66

57

9.2

47.6

26.4

61

 

H50_F1

0.948 ± 0.065

66

35

17.4

125.1

45.6

37

 

H50_F3

0.844 ± 0.189

66

78

8.3

233.0

28.6

67

 

H50_F4

0.891 ± 0.084

66

69

11.8

110.7

28.9

71

 

H50_F6

0.790 ± 0.256

66

47

16.9

155.5

43.9

36

 

IMAC_F1

0.939 ± 0.038

66

66

9.5

54.8

29.9

59

 

IMAC_F3

0.884 ± 0.112

66

57

13.1

65.6

34.1

39

 

IMAC_F4

0.911 ± 0.080

66

50

14.3

48.3

27.4

68

 

IMAC_F6

0.728 ± 0.265

66

55

9.7

66.8

35.4

36

B

CMHS_F3

0.940 ± 0.037

58

53

9.8

86.0

33.2

57

 

CMHS_F4

0.878 ± 0.085

59

41

12.1

89.1

34.7

44

 

CMLS_F1

0.946 ± 0.038

66

68

8.0

48.1

22.5

82

 

CMLS_F3

0.911 ± 0.059

57

75

7.2

45.4

23.9

77

 

CMLS_F4

0.941 ± 0.049

64

55

9.7

41.8

21.9

84

 

CMLS_F5

0.910 ± 0.060

63

52

10.4

47.8

24.2

77

 

CMLS_F6

0.935 ± 0.055

65

71

9.2

50.6

24.6

69

 

H50_F1

0.961 ± 0.037

65

83

14.3

131.2

49.4

24

 

H50_F3

0.922 ± 0.055

58

78

8.2

65.3

21.6

82

 

H50_F4

0.905 ± 0.068

63

69

8.5

111.8

26.9

74

 

H50_F6

0.922 ± 0.057

48

46

14.8

169.1

36.0

43

 

IMAC_F1

0.939 ± 0.038

66

66

9.5

54.8

29.9

59

 

IMAC_F3

0.925 ± 0.045

61

60

12.5

58.3

31.8

43

 

IMAC_F4

0.921 ± 0.061

65

50

14.2

47.4

26.9

68

 

IMAC_F6

0.929 ± 0.041

16

60

7.0

46.2

23.6

70

C

CMHS_F3

0.980 ± 0.018

58

53

8.1

50.4

19.1

92

 

CMHS_F4

0.971 ± 0.027

59

41

5.5

24.6

16.2

100

 

CMLS_F1

0.975 ± 0.026

66

68

5.3

30.0

15.1

100

 

CMLS_F3

0.961 ± 0.052

57

75

5.2

25.7

13.9

100

 

CMLS_F4

0.972 ± 0.039

64

55

5.9

26.2

14.4

100

 

CMLS_F5

0.979 ± 0.018

63

52

5.8

30.8

13.0

98

 

CMLS_F6

0.975 ± 0.024

65

71

5.2

42.3

15.8

96

 

H50_F1

0.990 ± 0.012

65

83

10.6

81.3

26.5

72

 

H50_F3

0.982 ± 0.012

58

78

5.8

40.4

13.5

95

 

H50_F4

0.977 ± 0.019

63

69

5.0

50.9

13.7

94

 

H50_F6

0.971 ± 0.028

48

46

7.1

51.8

17.1

91

 

IMAC_F1

0.976 ± 0.197

66

66

7.1

43.2

19.5

92

 

IMAC_F3

0.968 ± 0.045

61

60

8.6

33.5

19.3

95

 

IMAC_F4

0.945 ± 0.055

65

50

10.2

39.7

20.8

88

 

IMAC_F6

0.989 ± 0.009

16

60

2.5

29.0

7.7

100

  1. Pearson Correlation Coefficients were calculated on the entire spectrum prior to peak detection, the coefficient for the entire dataset is reported (Grand statistic). The coefficient of variation (CV) is calculated on all peak intensities.
  2. (A) All spectra in each QC sample data sets
  3. (B) Spectra remaining after passing diagnostic plot cut-off of 1-Mean r < 0.2
  4. (C) Spectra after Partek Batch Removal.