Predict fragments for several co-fragments isoforms and match them to a spectrum

[pavel-shliaha]

I have a histone peptide GKGGKGLGKGGAKR

that has 4 K residues. 3 of them are acetylated, so there is 4 potential isoforms: acetylations on 1,2,3 ; acetylations on 1, 2, 3 ; acetylations on 1, 2, 4 and acetylations on 2, 3, 4.

All 4 forms are co-fragmented. Most of the fragments are shared between some, but not all forms. What would be the easiest way to produce a table with all, -b and y- fragment masses for each form and then match these fragments with a given tolerance to a spectrum? The output I expect is 2 tables:

table 1:

rows are isoforms and columns are -b and -y fragment masses

table 2

rows are isoforms and columns are -b and -y fragment intensities from the matched spectrum