The Biemann nomenclature gives a mass difference of 17 Da between y and z ions. Why is Protein Prospector giving me a 16Da difference.?
You are correct that the mass difference between a y and z ion according to Biemann nomenclature should be 17Da. The confusion is caused by the fact that people describe ions as z ions, when they are not. Fragmentation mechanisms such as ECD and ETD do not form z ions, contrary to what you might think upon reading the literature. The predominant C-terminal fragment ion type formed is actually a z+1 ion (which differs from a y ion by 16 Da). Some people refer to this as a z• ion to indicate it is a free radical ion (which the z+1 ion is, but the z ion is not). To add to the confusion, it is also possible to form an ion where the z• ion abstracts a hydrogen to form what is generally referred to as a z+1, but according to Biemann nomenclature it would be a z+2 ion. So, Protein Prospector is reporting the mass of the ion you expect when doing ECD or ETD, which is commonly referred to as a z ion, although it is technically a z+1 ion.
