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"Library" peak area in replicate comparison graph

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"Library" peak area in replicate comparison graph stephen swatkoski  2019-03-01 07:21
 

Hi Brendan,

I acquired PRM data for 5 samples and I am using skyline 4.2.0.19009 to analyze the data. I used the option to load PRM database search results from the start menu page. I am very happy with the way the data looks but I am confused by the peak area that is labeled as "library" in the Peak Area Replicate comparison plot. How is the "library" area assigned? Is it the area of the best (most intense) peptide across the samples? Is there a document or tutorial that explains this?

Thanks,
Steve
 
 
Brendan MacLean responded:  2019-03-01 16:17

It is actually just the library proportions from the library applied to the maximum total peak area of your replicates, which allows you to get an eyeball view of how similar the proportions of the library and the measured chromatograms are. In other words a visual representation of what is reported in the "dotp" values. And it allows you to make observations like, "Looks like there was a lot more b7 in the library spectrum than the measured peak areas."

But, it is not an actual area. It is an expression of the expected relative abundances.

Hope this helps. Glad to hear you are very happy with how your data look.

--Brendan