If the peptides of interest are modified in a variable fashion it would be helpful to export this annotation in the results csv file as well (eg. by adding [Tri-Methyl]). Otherwise in the final list one has to discriminate the modification by hand on the basis of mass assignments. I am not sure whether this export option is already available in skyline and I just could not find it.
Thank you for your help.


2011-06-02    Brendan

Hi Sandra,
The reports do have the field:

Peptides.Precursors.ModifiedSequence

It is not in Peptides, as the modifications will be different between light and heavy precursors. I will keep this as a low priority Todo, however, sine this string only has modification masses:

AGLC[+57]QTFV[+5]YGGC[+57]R (2 carbomidomethylated Cysteines and one isotope labeled Valine)

And not the modification names, as you suggest. Hopefully this will be enough for you for now, however. It does pretty well distinguish different peptide modification forms.

Thanks for taking the time to give your feedback.

--Brendan

A Peptide.ModifiedSequence field was added a while now. It uses modification delta masses, though, and not the modification names.