|Ratio and area calculations in skyline||vabitsika||2017-02-13|
I am using Skyline (64 bit) 3.6.0 10162.
I am having some trouble to understand the calculations performed by Skyline, if I am using the correct exported light to heavy ratio and how can I export the raw areas. In the “export report” window I export the “Peptide Ratio results” and use the “ratio to standard” as the main quantification value. But how are the “ratio to standard” and the “quantification” values calculated?
I read your comment on the total area: that it is calculated as follows:
TotalRatio = LightArea1 + LightArea2 + LightArea3
HeavyArea1 + HeavyArea2 + HeavyArea3
How can I export this total ratio? In the precursor results summary: I only find the total area and the total area ratio. How are these calculated? FYI I checked this glossary (https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/CustomReports-2_5.pdf#page=32) and not enough information on the exact calculations is included.
Also how can I export the raw Light area 1, Light area2 …heavy area1 etc ( in the quantification setting, I have selected in regression fit: none and in normalization: none).
- One more point I would like to make is that the values in the “quantification” column do not seem to match with the observed areas of the transitions peaks: eg the highest transition is around 3.5 * 106 and in the respective exported file the quantification value is 1.16 * 107
- The final point I would like to make is that I get some NA in the quantification column of the heavy peptide when the spectrum of the heavy peptide looks good and ratio to standard is calculated fine (no NA). I can send you a report to see for yourself if that would be more helpful. How can this be solved?
Thanks a lot,