With the release of Mascot Server 3.0, Matrix Science has implemented a new file format, Mascot Search Results (MSR), which is the new default file format (an SQLite file). Mascot Server can still be configured to write DAT files, but your server/systems administrator or IT staff will need to make a configuration change on the server.
There are two ways to achieve this with Mascot Server 3.0 and write the results as DAT (*.dat) files (dat28 format).
1. Export the results in Mascot DAT format from the Protein Family Summary report. The export script (export_dat_2.pl) automatically converts MSR to DAT (dat28). This step can be scripted to export a batch of files
2. Enable the compatibility option AlwaysCreateDat28ResultsFile in the Configuration Editor. This option is documented in chapter 6 of the Installation & Setup manual