I have a really large search database, what search strategies do you recommend for searching my mass spectrometry dataset?

Readers are encouraged to use the database sectioning approach described by Praveen Kumar et al and available within Galaxy. Readers are also encouraged to consider other approaches such as MetaNovo (not yet available in Galaxy). In absence of any database or taxonomic information about the microbiome dataset, other methods such as COMPIL 2.0 and De novo search methods can also be considered.