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Table 3 Influence of factors specifying the pairwise peak-list comparison on partial areas under the ROC curve for binary PMF and MS/MS data. For each of the 96 pairwise comparison approaches, sensitivity-PAUC (sensitivity given FP-rate ∈ [0, 0.1]) and specificity-PAUC (specificity given sensitivity ∈ [0.9, 1]) (Figure 2) were determined. A partitioning of sums of squares was performed analogously to analysis of variance. Column names: Factors – identification of factors; df – degrees of freedom (DF, number of factor levels – 1); %SSQ – relative sum of squares (%SSQ = SSQ/∑SSQ); %MSQ – relative mean sum of squares (%MSQ = MSQ/∑MSQ), where MSQ = SSQ/DF. %MSQ measures the importance of a specific factor for the size of specificity-PAUC and sensitivity-PAUC. × denotes interactions between factors. measure – distance measure, noncross – non crossing matching, length – alignment length, θ – weight of non-matching peaks, residual – unexplained %SSQ or %MSQ, total – column sum of %SSQ, df, %MSQ.

From: Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process

  

PMF

MS/MS

  

specificity – PAUC

sensitivity – PAUC

specificity – PAUC

sensitivity – PAUC

 

Model with main effects

Factors

df

%SSQ

%MSQ

%SSQ

%MSQ

%SSQ

%MSQ

%SSQ

%MSQ

measure

3

10

14.9

10.9

16.1

4.4

8.5

2.7

5.5

θ

2

17.3

38.1

17.0

37.7

14.3

42.0

15.9

48.2

length

1

10

43.9

9.7

43.0

6.4

37.3

5.8

35.4

weight

1

0

0

0

0

0.0

0.2

0.4

2.2

noncross

1

0

0

0

0

1.2

7.1

0.6

3.5

residual

87

62.5

3.2

62.4

3.2

73.7

5.0

74.6

5.2

total

95

100

100

100

100

100

100

100

100

 

Final model N

Factors

df

%SSQ

%MSQ

%SSQ

%MSQ

%SSQ

%MSQ

%SSQ

%MSQ

measure

3

10.2

8.5

10.9

9.2

4.4

4.8

2.7

3.0

θ

2

17.3

21.7

17.0

21.5

14.3

23.6

15.9

26.0

length

1

10.0

25.0

9.7

24.5

6.4

21.0

5.8

19.1

measure × θ

6

7.5

7.3

17.7

7.4

16.3

9.0

17.2

9.4

measure × length

3

10.1

8.4

10.0

8.4

7.3

8.0

6.5

7.1

θ × length

2

17.3

21.7

17.0

21.5

14.4

23.8

15.6

25.6

measure × θ × length

6

17.5

7.3

17.7

7.4

416.0

8.8

16.4

8.9

residual

72

0

0

0

0

20.9

1.0

19.9

0.9

total

95

100

100

100

100

100

100

100

100