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Note that letters/residues B, J, X and Z have zero mass and can be used as a custom residue by specifying a modification mass for it. U is selenocysteine and O is pyrrolysine. Also, all lower case letters (except for c, e, h, n, o, p, s which have elemental masses assigned to them) also have zero mass and be used as custom residues. For example, 2-Hydroxyproline is C5H9NO3 which has mass 131.058243 calculated using the Elemental Mass calculator. So use the lower case 'v' to represent 2-Hydroxyproline in the peptide sequence and specify '131.058243@v' as a user defined modification.And if there is any extension that would be helpful in this fragmentation calculator, let me know and I just may implement it!

Set fragmentation parameters:
• mass type: mono avg
• product charge: 1 2 3 4 5 6 7 8 9 10
• fragment ion type: a b c x y z z•
• no mods
• use carbamidomethyl C (57.021464 mono, 57.0513 avg))
• user defined:
    #@AA or #@pos, i.e. "15.995@M 57.0215@3", space separated
    for addition to N-term use '[' and for C-term use ']', e.g. "16.0@["