massXpert

massXpert is a handy and easy to use mass spectrometry application especially designed to help you with your polymer sequences.

For the program to be able to cope with a variety of possibly very di erent polymers, it had to be written using some abstraction layer in between the mass calculations engine and the mere description of the polymer sequence.

This ab-straction layer is implemented with the help of \polymer chemistry de nitions", which are les describing precisely how a given polymer type should behave in the program and what its constitutive entities are. The way polymer chemistry de nitions are detailed by the user is the subject of a chapter of this book.

However, in order to give a quick overview, here is a simple situation: a user is working on two polymer sequences, one of chemistry type \protein" and another one of chemistry type \dna". The protein sequence reads\ATGC", and the dna sequence reads\CGTA".

Now imagine that the user wants to compute the mass of these sequences. How will massXpert know what formula (hence mass) each monomer code corresponds to? There must be a way to inform massXpert that one of the sequences is a protein while the other is a DNA oligonucleotide: this is done upon creation of a polymer se-quence; the programs asks of what chemistry type the sequence to be created is.

Once this \chemical parentage" has been de ned for each sequence, massXpert will know how to handle both the graphical display of each sequence and the calculations for each sequence.