TFA apart of being the strongest of these three, it has the ability to form H-bonds with its F-atoms and albeit possesses special catalytic properties.
It all depends why you need the sample for. If MALDI is the next step, you need to make sure you use a volatile acid, HCL is not, TFA and acetic acid are as well as formic acid
One can use Formic acid as well, for ESI Ionization we always use Conc. Formic acid (1-2ul). The acid also serves to protonate the peptides so that they ionize in solution and are easily detected in the Mass-spectrometer. TFA sometimes suppresses ionization in ESI-MS