Note: [] Address for correspondence: Institute of Informatics, University of Warsaw, 02-097 Warsaw, Poland Also works: Mossakowski Medical Research Centre PAS, Pawinskiego 5, 02-106 Warsaw, Poland
Abstract: In this paper we propose a mathematical model of the proteolysis process. Protein digestion is modelled with the use of chemical master equation (CME), i.e. the system of stochastic differential equations corresponding to the network of enzymatic reactions. We present an efficient approach to model parameters' estimation (i.e. enzyme activities) from time series of mass spectrometry data. These results extend previous results in three directions: by relaxing the stationarity of the proteolysis process assumption, by allowing cuts at arbitrary sites in the peptide sequence and by incorporating knowledge from biological databases.
Keywords: chemical master equation, peptidase activity, proteomics, stochastic modeling, mass spectrometry, Markov chain, non-linear optimization, matrix exponentiation
