SEARCHGUI PROTEOMICS MANUAL

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SEARCHGUI PROTEOMICS MANUAL

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 11 h. We added homemade java-script to automatize pipeline from file picking to report generation. We selected combination of X!Tandem, MS-GF + and OMMSA as the most time-efficient and productive combination of search. We also compared the results of our search combination with Mascot results using protein kit UPS2, containing 48 human proteins. 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 ( ) into total result of proteoforms identification and optimized set of engines working simultaneously. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. Nowadays, the routine manual search does not satisfy the “speed” of modern science any longer. Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data.

Searchgui proteomics