Table 1

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

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.

(A) All spectra in each QC sample data sets

(B) Spectra remaining after passing diagnostic plot cut-off of 1-Mean r < 0.2

(C) Spectra after Partek Batch Removal.

Whistler et al. Proteome Science 2007 5:14   doi:10.1186/1477-5956-5-14