CE optimization library different precursor and product z

CE optimization library different precursor and product z Erik  2020-01-03

Hi All,

I more often measure peptides that have a predominant breakage point (mostly proline) and thus the most abundant ions are formed from the same ion but in two different charge-states. Can I store the CE value of multiple product ion charges from the same peptide ion fragment (y6+ and y6++ for instance) in the library?
Similarly, but less relevant can I do the same for a peptide sequence with different precursor charge?

I was not able to find this anywhere in the tutorial or support forum. Hopefully this is possible without changing the software too much. I suggest one or two additional columns with precursor z and product z. Or is it possible to provide the charge in the "product ion" column?


Brendan MacLean responded:  2020-01-03

Hi Erik,
I assume you are talking about the Optimization library field in the Transition Settings - Prediction tab.

Charge state is supported there. This is all possible using + to denote charge, i.e. y6++ as you have used. We went a little cheap on the columns and the expressions, choosing to have "y6" be equivalent to "y6+", but because most peptides are charge 2, you should see PEPTIDER++ in the "Modified Sequence" column for most of them. Not sure if we would use just "PEPTIDER" for a singly charged peptide, but possibly.

I agree that it would be nice to have a way to switch to just showing the charge states (or adducts for small molecules) as separate columns. Perhaps we can add a checkbox for that at some point.

For the moment, however, you should be able to get what you are looking for once you understand the required format, which is pretty simple.

I have attached a screenshot of the Edit Optimization Library form when the CE Optimization tutorial is performed and its results are stored in an optimization library using Add > From Results. This is a great way to get examples of what Skyline expects. I will ask the developer responsible for the Optimization Library functionality to add this step to the CE Optimization tutorial.

Thanks for your feedback. Hope this covers what you were looking for.


Erik responded:  2020-01-06

Hi Brendan,

Thank you for your fast and adequate response! This is exactly what I needed to know and was not clear to me.