Table 2 Factors considered in the comparison process and their levels. Column 1 – Factors: identification of factors, Column 2 – Levels: short summary of the levels (For more details please refer to the Methods section). Column 3 – Number: number of levels. Int. – comparisons considering the intensities; Bin. – binary measures.

Int.

Bin

1

non crossing matching

yes

no

2

2

weighting match accuracy

yes

no

2

3

weight of non-matching peaks

0.5

1

2

3

4

intensity transformation

I

$\sqrt{I}$

log(I)

rank(I)

4

0

5

intensity normalisation

tic(I)

||I||

S(I)

Z(I)

4

0

6

alignment length

$M=M_1^X+M_1^Y-M_{11}^{XY}$

M = const

2

7

distance measure

See Methods Section

7

4

Product of levels for nonzero factors:

2688

96