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Methods used to control the quality of peptide products depend on the level of development of analytical and bioorganic chemistry, and the level of instrumentation. Peptide identification is a difficult task and largely depends on the complexity of its structure. There does not exist a comprehensive and simple test, except for NMR, which, however, is rather expensive and time-consuming and involves complex data interpretations. Moreover, it does not allow for unambiguous determination of the peptide purity and formula (amino acid composition, sequence, chirality of amino acid residues). For this reason, a combination of methods is often used, including amino acid analysis, TLC/HPLC and mass spectrometry, and, less frequently, sequencing. Current international practice of peptide analysis is to use HPLC in combination with mass spectrometric, mainly tandem (HPLC-MS/MS), detection. According to literature sources the amino acid sequence of linear peptides can be analysed using various enzymes and subsequent identification of proteolysis products by mass spectrometry. This article presents approaches to the development of test methods for analysis of purity and identification testing of a small interfering RNA-based novel medicinal product, which will help standardise and control the quality of the production process.