A research was conducted to on the induction of directed fragmentation of peptides and proteins by tandem mass spectrometry using 4-formylbenzenesulfonic acid (FBSA) and 4'-formylbenzo-18-crown-6-ether (4fb18C6). A prerequisite for achieving directed fragmentation is the covalent labeling of the N-terminus of the peptide. The analysis of the resulting products and fragment ions was carried out using a coupled system of nanoliquid chromatography and tandem mass spectrometry with electrospray ionization. The derivatization reactions, i.e. reductive amination, were carried out in an aqueous medium at pH 6 under microwave irradiation. Selective labeling of the N-terminus of peptides with FBSA enabled chemically activated fragmentation in both positive and negative modes of the mass spectrometer under charge reduction conditions. The rate of side reactions is almost negligible and the resulting data set ensured reliable de novo peptide sequencing. On the other hand, the labeling of peptides with the reagent 4fb18C6 and the overlap of fragment ions obtained from identical intact and derivatized peptides in tandem mass spectrometry allowed the reduction of chemical noise and the identification of proteins using the BLASTp algorithm by searching the NCBInr and UniProtKB/Swiss-Prot databases. The developed derivatization method with de novo peptide sequencing is a reliable method for the accurate determination of the primary amino acid sequence in peptides and represents a new tool for the identification of species by searching sequence databases.