How do Skyline calculate the light to heavy ratio?

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How do Skyline calculate the light to heavy ratio? Brendan MacLean  2009-12-10
 
Hi Brendan,
  
  I'm using Skyline to do quantitation work.But I don't know how do Skyline calculate out the ratio.So I write this message for your help.
  Any suggestions from you will be appreciated.


Thanks,
Zhang
 
 
Brendan responded: 2009-12-10 05:36
Hi Zhang,
The "ratio" number that appears in Skyline on the transitions is simply:

Ratio = LightArea / HeavyArea

The "total ratio" number that appears in Skyline on the precursors is weighted mean of the transition ratios, where the weight is the area of the internal standard, or heavy area:

TotalRatio = HeavyArea1*(LightArea1/HeavyArea1) +
             HeavyArea2*(LightArea2/HeavyArea2) +
             HeavyArea3*(LightArea3/HeavyArea3)
             -------------------------------------
             HeavyArea1 + HeavyArea2 + HeavyArea3

Which reduces to:

TotalRatio = LightArea1 + LightArea2 + LightArea3
             ------------------------------------
             HeavyArea1 + HeavyArea2 + HeavyArea3

But statistical calculations for standard deviation and standard error for weighted means still apply, using the HeavyArea weights expressed in the initial calculation.

We have seen experimentally that this TotalRatio produces the lowest mean/stdev values over a set of 10 replicates when compared with either using the ratio of the most intense transition or an unweighted mean of all transitions.

Hope this helps. Thanks for inquiring.

--Brendan