As of 5/30/08:

1. Incorrect syntax on the command line (e.g., leaving out the equals sign when specifying options) results in a crash.
2. Input files must be in the current working directory, i.e., the same directory where you type the mscout command. The program will run, but signal lists and histograms will probably not be generated.
3. Running MScout on high-resolution data will yield unpredictable results, if any results at all. Try specifying a low-resolution m/z setting (such as -mz=0.1), even though the data are high-resolution. Try Hardklör for high-resolution data.