Objective. To establish the most efficient protein search engines for the sequence identification of proteins derived from the formalin-fixed paraffin-embedded surgical tissue samples of colorectal cancer.

Materials and methods. The research was conducted on the surgical material of 10 colorectal adenocarcinomas from the 10 patients. Mass-spectrometry and the proteome analysis in the eight protein search engines (OMSSA, X-Tandem, MyriMatch, MS Amanda, MS-GF+, Comet, Tide, Andromeda) were used for the protein analysis.

Results. MS-GF+, X-Tandem and MyriMatch were the most efficient open-source protein search engines. Combination of two or more protein search engines allows to perform additional validation as well as to maintain high performance of the analysis. X-Tandem appeared to be not only one of the most productive protein search engines but also the fastest one.

Conclusion. MS-GF+, X-Tandem and MyriMatch combination in the protein analysis of tissue samples helps to increase the output of the protein search based on the technical organization of the algorithm without additional sample preparation and financial costs for the specialized soft.