Export MRM method into Sciex 5500 QTrap

Export MRM method into Sciex 5500 QTrap Richard Lam  2019-03-27

I generated the MRMs from peptides using Skyline and experienced an error when trying to export the MRM parameters into a method for Analyst (Sciex 5500 QTrap) - see attachment for the error message.


  1. I am using Analyst 1.6.3
  2. Skyline (64-bit)

Any solution to resolve the Export to Method issue?

Best regards,


Brendan MacLean responded:  2019-03-27

You can either just click "Yes", or you can set your CE predictor to "SCIEX" in Settings > Transition Settings - Prediction Tab. You may also want to set the DP predictor to "SCIEX", but if that isn't mentioned in the message, maybe you already have this set right.

It is not really an error message, more of a warning and an offer to use the expected default for a system of the type you have chosen.

Hope this helps clarify the issue.


Richard Lam responded:  2019-03-28

An error occurred after I click 'Yes' (see attachment for the error message).
Sorry, I did not include it in the previous inquiry.



Brendan MacLean responded:  2019-03-28

Hi Richard,
This is indicating that you don't have Analyst installed on the computer you are trying to use to export your method. Are you feeling that Skyline is mistaken and you actually have Analyst installed? Skyline checks the registry for a key that Analyst sets there in order to find the Analyst libraries it needs to export a SCIEX method.

You can solve this issue by either copying your file to an instrument control computer (with Analyst installed) and exporting your method there, or you can install Analyst on your non-instrument computer.

Skyline cannot export a SCIEX instrument method without an Analyst installation on the same computer. But, let us know if you think Skyline is just not finding an installation you believe you can find on the computer in question, and we can start digging into the registry keys on your computer to understand why they are not enough for Skyline to find the installation.


Richard Lam responded:  2019-04-01

You are right. I do not have Analyst installed in the computer that I am trying to use to export the method.