Hi, Brendan,
    Skyline is really great for MRM design and data analysis for large number of peptides. It will be very useful if there are more functions for data analysis. For example, there are four experiment conditions, each condition has 3 technique replicates, skyline can plot a graph to show the different condition results with average peak value plus error bar, like attached excel file shown. Thanks! zhijun
 
zcao

 graph for different conditions comparison.xlsx (document lost with hard-drive crash)


2011-04-29    Brendan
Yes. We do plan to cover cases like this and response curves with a set of features we have planned, but which we have not been able to get to yet. Without more resources, we can only go so fast.

Thanks for the input.

--Brendan

This suggestion is covered by replicate annotations and the group-by right-click menu item in the peak area plots. We are also working on fold-change statistics in Skyline, and we now have MSstats as an external tool.