Navigating through metaproteomics data: A logbook of database searching

摘要: Metaproteomic research involves various computational challenges during the identification of fragmentation spectra acquired from proteome a complex microbiome. These issues are manifold and range construction customized sequence databases, optimal setting search parameters to limitations in algorithms themselves. In order assess importance these individual factors, we studied effect strategies combine different algorithms, explored influence chosen database settings, investigated impact size protein used for identification. Furthermore, applied de novo sequencing as complementary approach classic searching. All evaluations were performed on human intestinal metaproteome dataset. Pyrococcus furiosus data contrast searching metaproteomic proteomic experiment. Searching against subsets databases use multiple engines increased number identifications. The integration P. sequences showcased limitation target-decoy-controlled false discovery rate combination with large databases. selection varying engine application represented useful methods increase reliability results. Based our findings, provide recommendations analysis that help researchers establish or improve workflows metaproteomics.