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The paper aims to develop an automated system that would ensure a robust peptide quantification process, which would permit researchers to quantify desired proteins faster and with greater reliability. Because of the uniqueness of the data used, biochemists' expertise and data mining methods were employed in this work. The system includes two main system components: one for the discovery of two quantification peptides and the internal standard peptide and the other for protein quantification in patient samples. If the required input data are available, each subsystem can be run separately. The developed system can be applied to similar problems because our design is flexible, allowing for easy adaptation.