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Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data. Nowadays, the routine manual search does not satisfy the “speed” of modern science any longer. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. We compared the contribution of each of the eight search engines (X!Tandem, MS-GF$+$, MS Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an open-source graphical user interface SearchGUI (http://searchgui.googlecode.com) into total result of proteoforms identification and optimized set of engines working simultaneously. We also compared the results of our search combination with Mascot results using protein kit UPS2, containing 48 human proteins. We selected combination of X!Tandem, MS-GF$+$ and OMMSA as the most time-efficient and productive combination of search. We added homemade java-script to automatize pipeline from file picking to report generation. These settings resulted in rise of the efficiency of our customized pipeline unobtainable by manual scouting: the analysis of 192 files searched against human proteome (42153 entries) downloaded from UniProt took 11h.

This paper presents a novel optimization algorithm, namely focus group (FG) algorithm, for solving optimization problems. The proposed algorithm is inspired by the behavior of group members to share their ideas (solutions) about a specific subject and trying to improve the solutions based on the cooperation and discussion. In the proposed algorithm, all the members present their solutions about the subject and all the suggested solutions proportional to their fitness, leave impact on the other solutions and incline them towards themselves. While trying to improve the quality of the candidate solutions, they converge to the optimal solution. To improve the performance of the proposed algorithm, two genetic operators are incorporated into the algorithm. The proposed algorithm is evaluated using several constrained and unconstrained benchmark functions commonly used in the area of optimization. Experimental results, in comparison with different well-known evolutionary techniques, confirm the high performance of the proposed algorithm in dealing with the optimization problems.