ion trap bruker and skyline

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ion trap bruker and skyline pucci biagio  2019-02-28
 

Hi,
I m new in skyline. i want to analyse file from .d bruker ion trap but i don't known how load these files in the skyline.
can help me?

 
 
Brian Pratt responded:  2019-02-28

Have you had a chance to go through any tutorials yet?

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials

Best regards,

Brian Pratt

 
Brendan MacLean responded:  2019-02-28

Specifically, you would want to be looking at the PRM tutorial, which seems like the only viable method on an ion trap instrument. This tutorial even covers PRM with an LTQ, which should be quite similar to what you might do with your Bruker ion trap.

https://skyline.ms/tutorial_targeted_msms.url

The other tutorials may also be useful in learning more about the general principals behind how data analysis with Skyline works.

I wouldn't really suggest trying to use ion trap data for MS1 filtering, which really requires modern high-resolution MS1 scans from a TOF or Orbitrap (or FT) instrument to get enough selectivity unless you are using highly purified samples.

Good luck getting started. Thanks for considering using Skyline in your research.

--Brendan

 
pucci biagio responded:  2019-03-01

thanks for answers..
but i don't understand how can import my ".d file" into slyline. i don't were able to do it!
all the best

 
Brendan MacLean responded:  2019-03-01

Then, you can't have looked at the tutorial. I think?

You import your .d file in the normal way with Skyline. File > Import > Results

But, you need to set up your targets and in the case of PRM, you would then export an instrument method, collect data specifically for your targets and only then import that data into Skyline.

If all you have is some DDA data you have collected on an ion trap, then Skyline is not the tool for you. You can review the tutorial on DDA data:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering

But, I wouldn't recommend trying this without high resolution mass spec data.

Hope this helps. You really will need to do some reading if you want to become an effective Skyline user.

--Brendan