FT-ARM only works with Thermo .raw files presently!
Step #1: Un-zip the download and open the GUI
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.