|Confusion with Skyline and Proteome Discoverer||Mark Athanason||2020-10-20|
First off thanks for providing the support that you do, hope I don't bother you all too much.
For right now I'm fine using the proteome discover software, but ultimately I want to perform DIA quant on similar data using skyline. Within PD, I perform a search using sequest and peptide validation with percolator with an FDR of 1%. Using the "import DDA search" wizard in the most recent version of skyline daily, I use the .msf file with a cut off score of 0.99. What I get in skyline doesn't seem to match what I see in PD at all. For example PD says I have 411 protein groups, but in skyline when I check remove repeat and duplicate peptides, I'm left with 222. Shouldn't these be the same since percolator is filtering for high confidence peptides? additionally, for some peptides PD does not correlate an MS1 trace where skyline does ... in my opinion incorrectly.
I'm uploading the .msf file, "Ibu1_DDA_1.raw" "Ibu1_DDA_2.raw" and "Ibu_DDA_3.raw" to https://skyline.ms/files.url
Any help would be greatly appreciated!