Since the middle of the 90s, mass spectrometry has evolved into an almost indispensable tool in structural studies on an ever-growing variety of (bio-)polymers, of which proteins, sugars and nucleic acids are the most prominent. Since the first public release of massXpert, the advances of mass spectrometry have motivated continuous and thorough maintenance of that software, in the form of two full software rewrites, culminating with massXpert 2, which we describe in this report. We shall describe the profound changes in massXpert that were performed so as to keep up with the technical advances in mass spectrometry since a decade.