Hi Yuqian,
I can't think of anything we have changed in this area. Can you have a look at Transition Settings - Prediction and report what you see in the "Collision energy" field? I have to admit that we have not yet added a "Thermo Altis" option in this list. The options for 3 triple quads are Thermo TSQ Ultra, Vantage, and Quantiva. I believe, the MacCoss lab uses "Thermo TSQ Quantiva" for our Altis. I definitely would not recommend either of the other 2 options for an Altis.

We will need more information about what you are using to get a better understanding of why your CE values have changed from what you were used to. Maybe look at an older Skyline document where you got values you were happy with and check that it has the same setting for CE as you are using now.

We have not changed the linear equations in these options, ever. So, it really must be that what you end up using has changed from before.

--Brendan

Thank you, Brendan! I think you are right. I normally didn't select anything in the transitions settings, and just leave it as "None". Maybe that is why it is causing some problems.

It could be. I really think we should make that error more explicit. In the case you describe, you would get the following message:

The settings for this document do not match the instrument type Thermo Altis:

Collision Energy: None

Would you like to use the defaults instead?

But what "defaults" exactly? Reading the code, it ends up taking the first settings in your list that start with "Thermo", which for a default installation is "Thermo Quantiva". So, that would work for you, and may have been what you were experiencing when you felt that accepting this message gave you values that worked on the Altis.

However, if you somehow ended up with a different list ordering where something else beginning with "Thermo" came before "Thermo Quantiva" then that could be a problem. I think we should be providing the name of the "defaults" Skyline will use to make that clearer.

Of course, your best option is to set what you want explicitly in Transition Settings and not accept the "defaults" which could vary from installation to installation of Skyline.

That makes more sense. I think making defaults more clearer in the error message is a great idea. Thank you so much!