The method uses the mapping assignments on the datset and replaces all identifiers with the assigned identifier of the mapping.

Example:

Assume you have protein abundance values for proteins and steady-state mRNA expression values in E.coli. Unfortunately the abundance values were provided with GenBank Identifiers and the mRNA expression values with Swiss-Prot Accessions. To test if mRNA expression and protein abundance correlates you must first find the corresponding values i.e. find the correct assignments of the GenBank- and Swiss-Prot identifiers. This can be easily accomplished by performing a BLAST run (or other mapping algorithms) of the GenBank Ids against the Swiss-Prot Identifiers (the sequences are retrieved automatically by PROMPT). As result you'll get the mapping of both identifier types. After checking or filtering the BLAST assignments, apply this mapping information to your protein abundance set. The GenBank Identifiers in the abundance set will now be replaced by the corresponding Swiss-Prot Identifiers and the mapped abundance values will be stored as new input object. Now your two inputs, the mRNA expression and the protein abundance data, have the same identifiers (Swiss-Prot) and you run a correlation test or other analyses.

Workflow of the apply-mapping example: