Citation of this work:
Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert. Bioinformatics. 2002, 18, 644.
Note that because the program has been rewritten over the years and the website has changed since the publication of the paper, mentioning http://www.massxpert.org along with the reference is certainly a good idea. A future article describing in detail all the new features will update everything.
Please, be sure to check regularly if the citation has changed or not.