FT-ARM only works with Thermo .raw files presently!

Step #1: Un-zip the download and open the GUI
You will need the raw file from your thermo instrument, the latest install of Xcalibur, and a .fasta database containing the sequences you'd like to search.

Step #2: Input the FT-ARM_segment.exe in the Executable dropdown

Step #3: Add .raw file and .fasta file pairs for searching

Step #4: Select desired search options and begin the searches
FT-ARM automatically searches both forward and reverse sequences input to estimate FDR in your dataset. This allows the user to decide where to apply a score cut-off dependent upon each individual dataset.