Libraries and targeted analysis


Hi Skyline Team,

I would like to ask you to answer my questions please.

1)     In the Proteome Discoverer, I uploaded raw data from MS, divided into three types and from these three types I created three libraries – each type had its own library. Is there any difference to upload all three libraries into Skyline, in which I evaluate the data of PRM analysis, or to upload them as one common library?

2)     We did targeted analysis on MS and the samples were measured in triplicates. Is it better, during the process of evaluation in Skyline, to do the average (total ratio) of all three replicates or just to select the most suitable replicate?


Thank you