A prospectus for tailoring metaproteomics database using MS/MS proteotyping
Résumé
Metaproteomics can be applied even to minute amounts of samples for which metagenomics cannot be performed due to the limited amount of material or the presence of degraded DNA as for some historical artifacts. In such cases, the database used for interpretation of MS/MS spectra can be constructed to represent the actual content of the sample. Although sequencing of 16S and 18S rRNA gene amplicons can provide an accurate list of genera or species, this approach is time consuming. It is now possible to bypass this step, as MS/MS proteotyping allows us to list the organisms actually present in the sample, as well as their relative biomass. Based on the most reliable peptide sequences, we can established with some confidence the taxonomic units present in a given sample. Metaproteomic interpretation can then focus on protein and function identification, avoiding many false positives due to searches of inflated databases. It is worth noting that this strategy is simply the basic tenet of proteomics: once proteins are extracted from a given organism, the database is chosen to represent only the protein landscape of that specific taxon.
Differentiating the concepts of "MS/MS proteotyping" and "metaproteomics" should help to improve discussions in our field and attract scientists interested in detection, diagnosis and forensics. This approach will be illustrated with very "unique" samples.