Table 4.

A summary table showing the advantages and disadvantages of the used algorithm for predicting the release of peptides during proteolysis.

Modeling Principles	Advantages	Disadvantages
Proteolysis is described in terms of concentrations of peptide bonds	The technique for determining the concentrations of peptide bonds during proteolysis is well established	In the transition from the concentrations of peptides to the concentrations of peptide bonds, a part of the information is lost
Proteolysis is characterized by the set of hydrolysis rate constants for enzyme-specific bonds	Quantification of rate constants for hydrolysis of peptide bonds is well tested	The determination of the hydrolysis rate constants is limited by accuracy of determining experimental curves
Demasking of peptide bonds during proteolysis is considered	Accounting for demasking improves the accuracy of proteolysis description	Precise determination of the demasking rate constants requires the use of new analytical methods
The size of peptide fragments is limited by trimeric blocks	The equations describing the release of peptides are relatively simple	The model does not describe the release of four-dimensional or longer peptide blocks.
The hydrolysis of slowly hydrolyzed bonds is not considered	The volume of calculations is reduced	The release of minor peptide fragments is not predicted