heavy/light targets

heavy/light targets moe  2016-10-12 16:00
Hi Skyline support,

Is it possible to insert a list of heavy peptides and associate with the existing target proteins? I wish to add/insert a list of 25 heavy SIS peptides (1 SIS per target protein) to my skyline document and associate them (I'm using a background proteome). The peptides may already be in the target list or not.

Is there a better way than doing this manually - i.e. is there an option where I can select a number of target peptides simultaneously and then change modifications for the selected items only rather than for the whole document?

If I go into peptide settings I seem to only be able to do this for the whole document. Same with the Edit -> refine -> advanced option, I can only remove/add labels for the whole document.

Brendan MacLean responded:  2016-10-12 16:12
Hi Moe,
Tricky. There is not really a great solution for you, I think, at the moment. You can definitely add peptides that will be associated with proteins in your background proteome through Edit > Insert > Peptides. I can't remember if they get dumped into existing proteins, if they are available, but I think so.

As for your exact use case, I might try something like.

1. Set up your heavy modifications to add heavy labeled precursors to everything.
2. Use Edit > Refine > Advanced to remove the heavy labeled precursors from everything.
(this will turn off auto-select at the precursor level for all peptides in the document)
3. Multiple select the peptides you are interested in and delete them all from the document.
4. Use Edit > Insert > Peptides to add them back.

Adding them back in step for should give them both light and heavy precursors again, since that is what you have the document set up for, but the other peptides have had their heavy precursors removed and then auto-select turned off.

This might get you where you are trying to go. Sorry, I can't think of anything simpler at the moment.

Good luck in setting up your experiment in Skyline.

moe responded:  2016-10-12 18:41
Thanks Brendan,

great support, your solution worked a treat, much appreciated!