Re: [spctools-discuss] TMT data analysis

[Jimmy Eng]

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, <ce.c...@gmail.com> 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 spctools-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.