You have 6 parameter values for your "variable_mod04" entry and 7 parameter values for your "variable_mod05" entry. One of them is wrong.
variable_mod04 = 6.03181 K 0 3 -1 0 variable_mod05 = 6.03181 n 0 3 0 2 0 As you mentioned the heavy lysines are identified correctly, you might also just try: variable_mod04 = 6.03181 nK 0 3 -1 0 The 'n' already implies n-terminal modification so you don't have to set the distance constraint at the peptide n-terminus as you meant to do in your "variable_mod05" entry. On Sun, Aug 23, 2015 at 7:32 PM, azelanis <[email protected]> wrote: > Hi all > > I am having issues regarding the analysis of Light (+ 28 Da) and Heavy (+ > 34 Da) di-methylation labeling using Comet through TPP v.4.8. > I tried to use the same approach of X!Tandem searches (ie. setting the > light di-methyl as a static modification for both N-termini and K and the > mass difference between the light and heavy dimethyl as a variable > modification for both K and [). > However, I noticed that in the pep.xml file only the light di-methyl is > present (at all N-termini), whereas Comet succesfully recognized the light > and heavy labels at K. > > Is there anything wrong with the parameters below? > > As variable modifications I'm using: > > variable_mod04 = 6.03181 K 0 3 -1 0 > variable_mod05 = 6.03181 n 0 3 0 2 0 > > As static mods.: > > add_Nterm_peptide = 28.031300 > add_K_lysine = 28.031300 > > > Any help would be very welcome! > > > > Cheers. > > > -- > 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/d/optout. > -- 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/d/optout.
