Thank you very much. This was really enlightening! On Saturday, February 15, 2014 10:41:59 AM UTC+2, Jimmy Eng wrote: > > This question comes up semi-regularly; here's the explanation obtained > from the author of X!Tandem many years ago: > > > http://tools.proteomecenter.org/wiki/index.php?title=TPP:X!Tandem_and_the_TPP#X.21Tandem_default_modifications > > > On Sat, Feb 15, 2014 at 12:04 AM, Konstantinos Vougas > <[email protected]<javascript:> > > wrote: > >> 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 >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> > >
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