Importing Data dawn dufield  2020-05-07
 

Hi I have 4 questions

  1. Is there a way to import acquired data that you don't have a skyline file for and have skyline automatically create transitions for those that are in the data file? vs creating it first in skyline and then importing. This would be much quickly for some small molecule data

  2. How does skyline handle Sciex Qtrap IDA data? If you acquire an IDA data file say for the top 4. Is there an easy way to review that data in skyline?

  3. When I'm integrating a specific peak and try to "apply to all" many times it does not still pick the same peak. How can I force this so I don't have to select each window in every file. (This is especially true when data is not great or peaks are noisy or low)

  4. What is the "best conditions" for transitions settings in your opinion for finding the best peptide to follow. Should you really cast a very wide window and use all transitions to last ion?

thanks
Dawn

 
 
Brian Pratt responded:  2020-05-07

Hi Dawn,

To answer your first two questions:

It's important to understand that Skyline is for targeted mass spec - the working assumption is that you have some idea of what was in the sample, probably as the result of using some kind of search software.

That said, you can easily use a spectral library to create a target list in Skyline, then refine your results to discard targets that clearly don't match the imported mass spec data. It's obviously a less sophisticated kind of search, but it sounds like you're comfortable with that.

Best Regards,

Brian Pratt

 
dawn dufield responded:  2020-05-18

how about #3? I seem many times to have to manually update each file

 
Kaipo responded:  2020-05-18

Hi Dawn,
This is something that is on our to-do list, but not yet implemented in Skyline.

Thanks,
Kaipo

 
dawn dufield responded:  2020-05-18

So there is currently no way to set a RT window and have it pick within that window?

 
Brian Pratt responded:  2020-05-18

Hi Dawn,

You can set an explict RT and RT window for each transition in the document grid (you'll want to reimport the data after you do). For small molecule data you can specify this directly in an imported transition list.

Best regards,

Brian

 
Brian Pratt responded:  2020-05-18

Hi Dawn,

I misspoke - RT is of course a per-peptide/molecule property, not per-transition.

Best,

Brian

 
Brian Pratt responded:  2020-05-18

Oh, and one more note - we recently made a change to how Explicit RT and Explicit RT Window work:

Formerly Skyline would use the Explicit RT information to choose the best peak within the provided RT window, and if no peak was found Skyline would pick the nearest peak even though it wasn't in the window, which was a surprise to most Skyline users. Now if no reasonable peak is found in the window Skyline simply doesn't pick a peak at all. So, you probably want to use Skyline-Daily.

Best,

Brian