Hello,
I have set the following modifications for an X!Tandem search in TPP:
<note type="input" label="residue, modification mass">57.021464@C</note>
<note type="input" label="residue, potential modification
mass">15.994915@M</note>
<note type="input" label="residue, potential modification
mass">15.994915@P</note>
<note type="input" label="residue, potential modification motif"></note>
<note> You can specify a variable modification only when present in a
motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N
only if it is present in an N[any but P][S or T] motif (N-glycosite).
</note>
<note type="input" label="protein, N-terminal residue modification
mass"></note>
<note type="input" label="protein, C-terminal residue modification
mass"></note>
<note> These are *static* modifications on the PROTEINS' N or C-termini.
</note>
... hence Carbamidomethylation of C as Fixed Modification and M & P
Oxidation as varible modifications and no N or C terminal modificaations.
In my results I get peptides like this:
R.*Q[111.03]*TVSWAVTPK.S
M.*n[43.02]*HGGGP[113.05]P[113.05]SGDSAC[160.03]P[113.05]LR.T
What are these Q[111.03] & n[43.02]. Actually I know that n[43.02] is
acetylated peptide alpha-amine but how come it is there?
Thanks in advance
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