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Capturing Proteolytic Activity in Mass Spectrometry Measurements
Stephan Aiche
Institute of Mathematics, Biocomputing Group, Freie Universität Berlin
E-mail : Stephan.Aiche(at) u-berlin.de
Abstract
Proteases are key players in a majority of biological processes. They are not only
associated with food catabolism but play also an important role in the regulation of
complex cascades like blood coagulation, cell cycle progression, and apoptosis.
Despite their importance they also play a problematic role in proteomic
measurements, since the ex vivo activity of proteases can destroy peptide profiles or
lead to incorrect conclusions based on peptide profile differences which are based
on degradation and not on a biological phenomena.
We therefore present an approach to identify proteolytic reactions in mass
spectrometry measurements. The identified reactants are organized in a network
and connected by the assumed reactions. The constructed network is used to
generate a mathematical model which characterizes the activity of proteolytic
reactions. The constructed mathematical model combined with time series
measurements is used to estimate the reaction parameters.
We present first results of this approach on simulated data that show a good
recovery of the original reaction system as well as the reaction parameters.
Abstract of talk
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