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PRM with skyline jung165  2017-12-21 03:07
 
First of all, I would like to appreciate for Skyline team's support

What I would like to ask is the parameters for full-scan for PRM analysis with Q-exactive (orbitrap)
I could find the tutorial for low-resolution (LTQ), but is it possible to imply those parameters for Q-exactive??

I tried to choose orbitrap on precursor mass analyzer(in full-scan tap) and it showed me to choose resolving power.
Should I have to set resolving power with same as that of Thermo Xcalibur Instrunment Setup??
I attached picture of those.

I am kind of confusing with those parameters for Q-exactive.
Is there any tutorial with Q-exactive (high resoution) experiment??
or can you give me any information about parameters for Q-exactive analysis

thank you very much for your help
 
 
Nick Shulman responded:  2017-12-21 12:04
You might want to take a look at the DIA tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dia
That tutorial involves data collected on an Orbitrap.

Yes, you probably should use the same resolution settings in the Skyline Transition Full Scan settings as you had on your instrument. The resolution setting in Skyline controls how wide of a channel Skyline sums across when Skyline is calculating the intensity that should be plotted on the chromatogram.

I believe our current recommendation is that you should choose "Centroided" for the mass analyzer, and then choose an appropriate mass accuracy depending on how the data was collected.

When you choose "Centroided", Skyline uses an algorithm provided by Thermo that looks at the shape of the curve in the scan, and figured out what it's total area and midpoint is. This is supposed to achieve better results than the usual way that Skyline sums the intensities across a channel.