#100 Implement amino acid-dependent neutral losses

[William S Noble]

Note: We should only implement this AFTER doing an empirical analysis of high-confidence PSMs to verify that these rules hold.

From Jimmy Eng:

Both b- and y-ions can lose water or ammonia. If you want to get even more specific, this is what I emailed Benjamin & Brendan MacLean back in June 2010 regarding neutral losses based on a literature search I did then:

A fragment can exhibit ammonia loss (-NH3) if it contains the residues K, R, Q or N.
A fragment can exhibit water loss (-H2O) if it contains the residues S, T, E or D.

Here's one brief description how/why from http://www.ncbi.nlm.nih.gov/pubmed/18092745

"Both the b ion and the y ion usually have a few variants since some amino acids in the peptide may lose a water or an ammonia. For a charged peptide, the water loss may be generated by dehydrating the −COOH group of the C-terminal Asp or the side chain of Ser or Thr. It has also been observed that the N-terminal Glu may lose a water. Compared with the water losing process, the pathway leading to ammonia loss is much simpler. It has been reported that the ammonia loss occurs on the side chain of Asn, Gln, Lys, and Arg."