Applied Biosystems Data Explorer 4 Series User Manual page 296

Chapter 6 Using Tools and Applications
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6-26 Applied Biosystems
Figure 6-15 Ion Fragmentation Calculator Dialog Box
4. Type or copy the amino acid or residue sequence of
interest. Use single-letter codes.
Sequence codes are case-sensitive. Click the
User-Defined Amino Acids button to display the list of
allowed residues and their associated codes.
5. Select the N-terminus and C-terminus options for the
sequence.
6. Specify the cysteine modification, and specify the mass
type (average or monoisotopic) for the calculated
fragment ion masses.