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List of instruments not visible in Instrument Tab under Transition Settings

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List of instruments not visible in Instrument Tab under Transition Settings vipinj1985  2025-03-19 05:38
 

Hi there,

I want to use Skyline software for Sciex 7500. I have downloaded the latest version of Skyline (24.1). However, I don't see the list of instruments in the Instrument Tab under Transition Settings to select Sciex 7500 (attached the screenshot). How can I make it visible to export transitions list for Sciex 7500 OS software? Am I missing something here? Your support will be greatly appreciated.

Best,
Vipin
 
 
Nick Shulman responded:  2025-03-19 06:54
You only need to tell Skyline which instrument you have when you are actually exporting a method or a transition list.
That is, when you use the menu item "File > Export > Transition List" there is a "Instrument Type" dropdown where you can choose "SCIEX".

Similarly, in the "File > Export > Method" window there are four different SCIEX instrument types:
SCIEX QQQ/QTRAP - Analyst
SCIEX QTOF - Analyst
SCIEX QQQ/QTRAP - SCIEX OS
SCIEX QTOF - SCIEX OS
For a triple quadrupole instrument like the 7500 I imagine you are supposed to choose one of those "SCIEX QQQ/QTRAP" instrument types.

There are many Skyline tutorials to help you get started. I would recommend the "Targeted Method Editing" and "Targeted Method Refinement" tutorials on this page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials
-- Nick
 
vipinj1985 responded:  2025-03-19 10:37
Thanks, Nick.

So, the CE calculated by skyline would be same for 6500 and 7500 QQQ? Also, when I am trying to import the transition list generated by Skyline into Sciex OS software, I am getting a message that number and order of columns in mass table should match. The transition list is compatible with Sciex Analyst mass table columns, but it doesn't match the OS mass table both the number and order of columns. Could you suggest how to tackle this issue? Is there a tutorial on 7500 or Sciex OS software?

Best,

Vipin
 
Mike MacCoss responded:  2025-03-19 11:47
It is your best best for a starting collision energy equation. The equation is customizable to your specific instrument and setup. We have a paper describing the process.
https://pubmed.ncbi.nlm.nih.gov/21090646/
And a tutorial
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_optimize_ce

Cheers,
Mike
 
vipinj1985 responded:  2025-03-19 12:14
Thanks, Mike.

Could you please let me know how to export the transitions list compatible with the Sciex OS software? While trying to import the current transitions list, I am getting an error message saying that the order and number of columns between the skyline transitions list and mass table in the software do not match.
 
Mike MacCoss responded:  2025-03-19 13:18
Hi ... have you tried the File > Export > Method? That should be the first place to start as Nick suggested. You give Skyline a template instrument method file and it should add the transitions directly into the method. The transition list is normally used when we can't export a method file directly. If we know more details about the columns expected, then I am sure that can be fixed fairly easily.

-Mike