providing a list of modified peptides

providing a list of modified peptides pavels  2019-01-03

I understand that it is possible to paste a peptide together with its transitions (as shown in the videos and tutorials), but can I load modifications as well? E.g. if I have many peptides with different modifications, could those be introduced in a column e.g. Y3P and K4me1 to also make them modified or do I have to go through them manually one by one and introduce the desired modifications?

Nick Shulman responded:  2019-01-03
When you do:
Edit > Insert > Peptides
you can specify a modified sequence in the "Peptide Sequence" column.

Skyline has many different ways of specifying modified sequences, but the simplest is to include the mass difference in square brackets. For example:

I believe you can also specify modified sequences when you do:
Edit > Insert > Transition List

I hope this answers your question.
-- Nick
Brendan MacLean responded:  2019-01-03
This thread has a bit more detail on what else is possible:

Note that SCIEX 3-letter codes are now supported and have been for a while.