How to normalize the peak area with b-gal peptide drrenugoel  2019-09-30
 

I would like to normalize the peak area with one peptide of b-gal which we had added in all teh samples
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 5550 C27_MRM
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 3340 C8_MRM
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 3131 C84_MRM
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 1516 M40_MRM
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 2315 S45_MRM
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 1592 S59_MRM
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 1531 S66_MRM
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 1845 S69_MRM
sp|P00722|BGAL_ECOLI APLDNDIGVSEATR 2979 S74_MRM

There is a variation in the peak area. How to normalize all other sample peptides by this peptide?

Thanks,
Renu

 
 
Brendan MacLean responded:  2019-10-04

Hi Renu,
This is what is known in Skyline as a Global Standard. See the section titled "Global normalization standards" at the bottom of page 29 in the Grouped Study Data Processing tutorial:

https://skyline.ms/_webdav/home/software/Skyline/@files/tutorials/GroupedStudies1-3_1.pdf#page=29

Once you have this set up, Skyline will also allow you to choose normalization to Global Standard in the Peptide Settings - Quantification tab.

Skyline also supports the use of Surrogate Standards, which allows you to specify a target as a standard and then explicitly choose which other targets it should apply to. You can read more about that here:

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

Hope this helps in reducing technical variance in your acquired data.

--Brendan