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Transition List dspiciarich  2018-04-13 16:37
 
I have a number of transition lists made on an Agilent QQQ that I would like to use in skyline for quantification but many of my peptides have complex post translational modifications

For Example:

PEPT[large glycan] IDE PrecursorMz FragmentMz

The fragments may include the glycan portion and not the peptide portion. I ideally would like to do this without putting in the amino acid sequence but just a name and a precursor and fragment m/z mass. Is this possible?

Last question, I have the precursor mass and the fragment mass and the glycan mass but sometimes would like to use the average mass, whereas other times want to use the monoisotopic? Is this possible?

Happy Weekend!

Thank you,
David
 
 
Brian Pratt responded:  2018-04-13 17:07
Hi David,

Skyline's small molecule transition list import can work with just name, mz and charge, yes.

I'm not sure I understand the last question, but it's easy for Skyline to work with either monoistopic or average mass if you have chemical formulas.

Thanks for using Skyline!

Brian
 
Brendan MacLean responded:  2018-04-15 11:12
Skyline also supports charged losses for peptides, which was requested by researchers working with glycans. So, you might just want to have a look at that, rather than giving up entirely on peptide sequence information and using "small molecule" transition lists. You can define custom fragment ions for peptides in the Transition List - Filter tab under "Special Ions". By default we have defined this type of ion for ICAT and TMT, but you can add whatever custom ions you like, by clicking the Edit List button. You might start by editing the ICAT and TMT ions to see how they are defined.

Hope this helps. Good luck measuring glycans with Skyline.

--Brendan