The documentation is available in the User's Guide:
Also, there is a journal article on ProtoFit in Computers & Geosciences:
Link to downloads of older versions and older documentation
A poster on ProtoFit's methodology and applications was presented at the V.M. Goldschmidt Conference in Moscow, Idaho. It is reproduced in html format on this website.
Further help can be obtained by contacting the author (Ben Turner).
Turner, B. F., and Fein J. B., ProtoFit: A program for determining surface protonation constants from titration data. Computers & Geosciences 32 (2006) 1344-1356.
Turner, B. F., ProtoFit Version 2.0, a Program for Determining Surface Speciation Constants from Titration Data: User's Manual, (2005), 27 p.
Turner, B. F., ProtoFit Version 1.0, a Program for Determining Surface Speciation Constants from Titration Data: User's Manual, (2004), 23p..
Turner, B. F., and Fein, J. B. (2005). A derivative method for analysis of surface potentiometric titration data and model optimization. Geochim. Cosmochim. Acta, 29 no. 10, suppl.1, p. A49.