Today I went through all my setting and files in Skyline for the 2015Oysterseed proteomic project and re-did my Skyline Daily peak-picking error rate determination. I still got an error rate nearing 50%, so per Emma’s suggestion, I submitted the issue to Skyline’s support page.
Here is a link to the Skyline Support page where you can find what I posted: https://skyline.ms/project/home/support/begin.view?
My error rate is near 50% in all four samples. Not good! Laura and Yaamini had final admissable error rates of 30%. I emailed Emma and she said that I should post to the Skyline support page… waiting to hear back from them now. Hopefully this can get sorted out soon. I would love to be able to move forward with the analysis and get more involved in this project.