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]>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]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > -- 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]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
