An article published in MicrobiomeJ presents metaSpectraST: an unsupervised, database-independent workflow that enables rapid microbial community profiling without the need for constructing the protein sequence database to analyze metaproteomic data.
]. The iProphet and ProteinProphet estimated false discovery rate were both set to 0.01. The metagenome-derived protein sequence database, constructed as described above, was searched to identified peptides/proteins expressed in the microbial communities. Thereference proteome was searched to identify peptides/proteins expressed by the host. The search database was appended with an equal-size decoy sequence database by the decoyFastaGenerator function of the Trans-Proteomics Pipeline .
The rationale behind this reconciliation scheme is threefold: database search with its relevant statistical validation is the most robust and reliable method in terms of peptide/protein identification, especially when sample-specific protein sequence database is available; open modification search also relies on the reference protein sequence database, albeit a more general one encompassing all bacterial proteins in Uniprot, and should be able to identify closely related sequences that are not...
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