How do people typically store LC/MS data for compound plates? Our LC/MS 96-well plate experiments are around 1GB, but I noticed a 180MB per file limit.

Our recommendation wrt to large binary data files is to store the files on a shared network location and store a pointer to the data location in the database. We do have some scripts to import data into database (see Scripts/Database in the Mnova menu). We will be very happy to develop custom scripting solutions for any functionality which is not met by the default import scripts.