Contaminants

The presence of contaminant proteins in proteomics samples is well established. The best way to identify contaminants in your data using the MetaMorpheus is to use a separate contaminants database in your searches. Users can easily incorporate the MPI contaminant database in their search by clicking the "Add Default Contaminants" button below the Protein Databases window.

The assignment of peptide spectral matches is prioritized to decoy first, then contaminant and last to target. In this way, you can be certain that your results are free from false positive artifacts.