The spectrum viewer has nothing to do with your database search i.e. it knows nothing about how you did a search and whether you applied a minimum fragment m/z or not. Nor does it know anything about TMT reporter peaks. It simply calculates fragment ions based on the peptide sequence and labels any peaks in the MS/MS scan corresponding to those calculated masses. If a calculated fragment ion happens to correspond to a peak in the spectrum that's a TMT reporter ion, it will label it as a fragment ion. If you know it's a TMT reporter ion that shouldn't be labeled, simply ignore the peak label.
On Wed, May 8, 2013 at 2:03 PM, <[email protected]> wrote: > Hi, everyone > > We’re presently having an issue when analyzing TMT data on TPP. On some > MS/MS spectra opened on the spectrum viewer, the algorithm seems to be > using the TMT m/z values to calculate the sequences of peptides (mainly > attributing a +3 charge to these values). We tried to change the k-score > and tandem parameters, setting it to "spectrum, minimum fragment m/z = > 150", but it didn’t work. Can anyone shed some light on how to solve this > issue? > > Thank you. > > Carlos > > -- > 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?hl=en. > 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
