how skyline do the peak picking

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how skyline do the peak picking xue shi  2021-12-07
 

Dear Skyline team,
I am using skyline to process Agilent QQQ MRM data now. However, could you please let me know how skyline integrate and calculate the peak area
Let's see for this transition, it has different retention time. Do you just add all the area with same transition 104.07- 58.196 together or you did some fittings(gaussian,EMG) for the peak picking?
PrecursorMZ ProductMZ
104.07 58.196

9.4305
9.44131667
9.44131667
9.44131667
9.45213333
9.45213333
9.45213333
9.46295
9.46295
9.46295
9.47375
9.47376667
9.47376667
9.48456667
9.48456667
9.48456667
9.49538333
9.49538333
9.49538333
9.5062
9.5062
9.5062
9.51701667
9.51701667
9.51701667
9.52783333
9.52783333
9.52783333
9.53865
9.53865
9.53865
9.54946667
9.43026667
9.44108333
9.44108333
9.44108333
9.4519
9.4519
9.4519
9.46271667
9.46271667
9.46271667
9.47353333
9.47353333
9.47353333
9.48435
9.48435
9.48435
9.49516667
9.49516667
9.49516667
9.50598333
9.50598333
9.50598333
9.5168
9.5168
9.5168
9.52761667
9.52761667
9.52761667
9.53843333
9.53843333
9.53843333
9.54923333
9.54923333
9.54923333
9.56005
Thank you a lot

 
 
Nick Shulman responded:  2021-12-07
Your SRM data file has two chromatograms with Q1=104.07 and Q3=58.196.
When Skyline reads the chromatograms from the data file, Skyline will only use one of those two chromatograms, and will ignore the other one.

Here is a page that talks about how Skyline does background subtraction:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tip_peak_calc

Skyline does not do any sort of curve fitting when calculating peak areas. The points along the chromatogram do get interpolated in the retention time dimension, but that has a very small effect on the peak area. The "Skyline Ecosystem" paper talks a little bit about this resampling in the section "B. Resampling":
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799042/

I hope that answers your question. Let us know if you have any other questions.
-- Nick