Instrument Platforms

Instrument Platforms amruta indapurkar  2018-12-14

We have a skyline software and we wanted to add some new instrument platforms to it, so that we can analyze data from multiple instruments. The instruments that we want to add to our software are:

  1. Thermoscientific Q-Exactive High resolution mass spectrometer
  2. Agilent’s 6530 Accurate Mass Q-TOF LCMS

I was wondering if that would be possible. Please let me know. Thank you.

Brendan MacLean responded:  2018-12-16

Hi Amruta,
Skyline should support these instrument platforms without your needing to do anything extra. You should be able to just start working with the data files these instruments produce and export the methods or isolation lists they require.

Thanks for posting to the Skyline support board.


amruta indapurkar responded:  2018-12-17

We already did that but we are experiencing problem. When we import the raw files from the Thermo QExactive, we are seeing a message that says, "Chromatogram uavailable". Is there any procedure to work with high resolution data in skyline? I don't think we have the isolation lists for thermo q exactive. Could you please let us know how to resolve this issue?

Brendan MacLean responded:  2018-12-17

The MacCoss lab and many others have done extensive work with Thermo Q Exactive data in Skyline. There are many materials for learning more about it. What sort of acquisition method have you used on your instrument? DDA, DIA, or PRM?

A great place to start of Orbitrap-based PRM would be the Skyline Tutorial Webinar on PRM with a Fusion Lumos:

What you are trying to do is very well supported in Skyline, but you are going to need to seek out the available instructional materials and put some effort into studying.

Thanks again for posting to the Skyline support board.