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Small Molecule Peak integration issue with Thermo .raw QE+ data

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Small Molecule Peak integration issue with Thermo .raw QE+ data prasadpb  2018-04-17 09:42
 
Dear Skyline team,

I am facing peak picking and integration issue with the skyline with small molecule LC-MS data acquired on QE+ system.
I have attached images of 13C Creatinine peak integration done on Skyline (small molecule feature) vs Thermo Xcalibur software.
With the same files, I found there is a huge difference in pick detection and integration.
Can you please guide regarding what I am doing wrong?
Is there any steps I am missing or how can refine the peak detection method better.

Thanks and Regards,

Prasad Phapale
EMBL, Heidelberg, Germany
 
 
Brendan MacLean responded:  2018-04-17 10:44
The chromatograms extracted by Skyline look quite a bit different from the ones from Thermo. What are your Transition Settings - Full-Scan settings like?

Note that the Xcalibur extraction range appears to be:

113.05327-113.05553 = 0.00226 m/z (centered on 113.0544)

So, the center is correct, but I would imagine that Skyline is not extracting the same range. You can check the range that Skyline is using with View > Document Grid, select Views > Mixed Transition List and then inspect carefully the "Full Scan Filter Width" column near the right end of the grid.

For one test I just tried this with the default centroided extraction of 10 ppm yields about 0.003 for a transition with 155 m/z. That seems pretty close to what you have. Maybe you are not using centroided extraction in Skyline?

Thanks for posting to the Skyline support board.

--Brendan