What is the purpose of TFA in mobile phase? Is there an alternative?

Based on my understanding, this is a typical MS additive. It is used to lower the pH of your mobile phase (without using a salt buffer), as opposed to using another type of acid to lower the pH that would require a salt to maintain the buffer at that pH.

http://www.ionsource.com/tutorial/chromatography/rphplc.htm

Go to the part describing solvents.

The purpose of TFA in the mobile phase can be for one of two purposes. The first purpose mentioned above by Keith,Q is to lower the mobile phase pH, generally for the purpose of enhancing retention of acidic solutes through suppression of ionization. For this application, TFA is a poor choice when the detector is UV at low wavelengths (since TFA absorbs significantly at low UV wavelengths) or MS (since it frequently causes problems in the MS interface due to its long term persistence). For this application, there are better choices such as MSA or phosphoric acid in the case of low wavelength UV detection or formic acid in the case of MS detection.

TFA is also frequently added to the mobile phase as an "ion pair reagent" where it's purpose is to enhance retention of cationic species. Although one might argue that TFA isn't a true ion pair reagent, it is probably the best choice of available volatile ion pair reagents for MS. In the case of UV detection, however, true ion pair reagents such as heptane sulfonate provide better retention enhancement of cationic species and are transparent in the UV.