Importing iRT values Erik  2019-11-07 07:24
 

Hi Skyline team,

For importing srm/mrm assays nowadays it becomes more regular that together with Q1/Q3 coordinates also the iRT is provided.
Is it possible to import a list of (oxi/phospho modified) peptides with their iRT?
I know you can import an iRT peptide database to an iRT calculator but this is only possible when you have measured the peptides yourself and export them as an iRT database .
So ideally when you first want to run an SRM assay with >100 peptides you can already let skyline predict the RTs based on iRT and export a method to measure the data with wide RT windows. It would be nice to be able to import an excel list with two columns [modsequence] [iRT] like you can also do with Q1/Q3 coordinates.

Hopefully you have a solution so I do not have to run many unscheduled runs first to let skyline know the iRTs of my peptides of interest!

Kind regards,
Erik
 
 
Brendan MacLean responded:  2019-11-07 07:58

Hi Erik,
This was an original feature requirement of the Edit iRT Calculator form, because the Aebersold lab had accumulated so many iRT values already that we wanted to make it possible for them to just paste into the form. I don't think we have broken this, and that you can still click on the grid and use Ctrl-V to paste a 2-column list of values from Excel (or just tab-separated from a text editor).

Let us know if this is not working for you, and we can look into what you are doing further. Otherwise, I would expect this to work with Ctrl-V to paste.

Good luck with your research. Thanks for posting to the Skyline support board.

--Brendan
 
Erik responded:  2019-11-07 08:27

Hi Brendan,

Thanks for your fast reply.
Before I tried this as well but then it did not work.
However, now simply copy-pasting a table in the extra peptides did the job!

Cheers,
Erik