New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

3.7. IDENTIFYING POTENTIAL FEATURES 51
Figure 3.7.16: This shows identified masterpeaks of two groups (top: men; bottom:
women). The alignment process assigns pairs of masterpeaks having similar properties
(such as m/z value). These assignments are indicated by the red arrows.
Algorithm
From the preprocessing steps we have acquired a list of masterpeaks of groups
G1, G2 (e.g. cancer group vs. healthy group). To obtain a set of masterpeaks
that differ in some defined property (e.g. average height) we perform the
following key steps:
i) Alignment of Masterpeaks in G1, G2 (masterpeak alignment across groups)
ii) Calculation of aligned Masterpeak Pair (MPP) property Jensen-Shannon
(JS) differences
iii) Order this list by distances.
This yields a list of pairs of aligned masterpeaks of G1 and G2, ordered by
their respective distances.
Pseudocode
The basic process is as follows:
Algorithm 4 Extracting features
Require: Lists of masterpeaks of group 1 & 2, respectively.
{Masterpeak Alignment}
Match the masterpeaks of group 1 & 2 by algos described in section 3.7.1.
{Calculation of Masterpeak Property Differences}
return A sorted list containing tuples of aligned pairs of masterpeaks with
their respective distances.
Preprocessing 1: Masterpeak Alignment (Across Groups)
The majority of masterpeaks obtained by the preprocessing steps occurs in
each group of spectra (e.g. S1, S2) at the same position and having identical
heights, due to the almost identical blood proteome of two humans. Remember