```CH908, Problem set 8. Collisionally Activated Dissociation (CAD) of
peptides
1. Memorize the structures of the 20 naturally occurring amino acids.
2. In the mobile proton model of peptide fragmentation, the initiating
event (after collisional activation of the molecule) involves a proton
transfer. From where? To Where?
The proton is normally on Arginine &gt; lysine &gt; histidine &gt; n-terminus &gt;
backbone amides. If it's on arginine or histidine, it's stuck and doesn't
move, so fragmentation of such peptide ions is poor. If it's elsewhere,
it can transfer to the backbone amide to initiate cleavage. This results
in a one Da transfer from nominal &quot;b&quot; ions to nominal &quot;y&quot; ions.
3. Calculate the CAD fragments that would be expected from the
following peptide sequence: RGHTTPSDELWIVK. What can you say
about expected relative cleavage intensity? Create a table of the
expected fragments and mark them with &quot;strong, medium, weak&quot; for
expected intensities.
Fragmentation next to proline (b6, y9) will probably be intense, as will
cleavage next to aspartic acid (b9, y6). For the rest, it's safest to just
call them &quot;medium&quot;, except for cleavage at glycine which will be weak.
4. Calculate the CAD fragments that would be expected from the
following peptide sequence: RGHTpTPpSDELpYIVK. Note: pS, pT,
and pY refer to phosphoserine, phosphothreonine, and
phosphotyrosine, respectively. What can you say about expected
relative cleavage intensity? Create a table of the expected fragments
and mark them with &quot;strong, medium, weak&quot; for expected intensities.
Since this peptide is triply phosphorylated, it's likely to be poorly
observed in positive ion mode, but nicely detectable in negative ion
mode. In positive ion mode, the same rules as above apply, but you
should also see several intense losses of phosphoric acid (-98 Da),
several water losses. Because of these losses, other backbone
fragmentation will probably be weak, but it will be evenly distributed
because of the abundance of mobile protons.
5. What's wrong with this picture?
The z and x ion cleavages are wrong, they are swapped. The rest are
correct.
a/x, b/y, c/z go together.
```