Hi,
I am trying to anlysis itraq8 Ms/Ms data with xtandm, and got confused by
a previouse disscussion iTRAQ data through xtandem! using TPP.
<https://groups.google.com/forum/#!searchin/spctools-discuss/tandem$20parameters|sort:date/spctools-discuss/e4wihr_i8JE/1SNYto9jMVgJ>
Should not the parameters in tandem.paraams.xml like follows,since balance
groups have been removed by the second Ms
<note type="input" label="residue, modification mass">57.021464@C</note>
<note type="input" label="residue, potential modification
mass">15.994915@M,8.014199@K,10.008269@R</note>
<note type="input" label="residue, modification mass 1">113@K</note>
<note type="input" label="residue, modification mass 2">114@K</note>
<note type="input" label="residue, modification mass 3">116@K</note>
<note type="input" label="residue, modification mass 4">117@K</note>
<note type="input" label="residue, modification mass 5">118@K</note>
<note type="input" label="residue, modification mass 6">121@K</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
1">113@K</note>
<note type="input" label="protein, N-terminal residue modification mass
2">114@K</note>
<note type="input" label="protein, N-terminal residue modification mass
3">116@K</note>
<note type="input" label="protein, N-terminal residue modification mass
4">117@K</note>
<note type="input" label="protein, N-terminal residue modification mass
5">118@K</note>
<note type="input" label="protein, N-terminal residue modification mass
6">121@K</note>
Sincerely,
Richard
<https://groups.google.com/forum/#!searchin/spctools-discuss/tandem$20parameters|sort:date/spctools-discuss/e4wihr_i8JE/1SNYto9jMVgJ>
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